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+d(c$,"NewTreePanel",function(a,b,c){if(!this.viewport.getAlignment().isAligned(!1)){for(var f,l=this.viewport.getAlignment().getWidth(),d=0;dd.getSize()){b.add(l,c);break}}b.contains(c)||b.add(c)}f=new java.util.ArrayList;for(d=0;dd[e]&&(g=d[e]))):f[e]=!1}if(0!=l){if(lz||null!=a&&!jalview.analysis.AlignmentSorter.containsIgnoreCase(s[v].type, +a)||null!=b&&null!=s[v].getFeatureGroup()&&!jalview.analysis.AlignmentSorter.containsIgnoreCase(s[v].getFeatureGroup(),b)?(s[v]=null,t--):!g&&!Float.isNaN(s[v].getScore())&&(0==m[e]&&u++,m[e]++,x[e]=!0,D[e]+=s[v].getScore());p[e]=y=Array(t);if(0D[e]&&(q=D[e])))}if(d===jalview.analysis.AlignmentSorter.FEATURE_SCORE){if(0==u)return;if(ul){for(h=0;h=c&&(c=String.fromCharCode(c.charCodeAt(0)-32)),"a"<=e&&"z">=e&&(e=String.fromCharCode(e.charCodeAt(0)-32)),c!=e&&(n?d?f--:l||h++:h++);return 1>f?0:100*(f-h)/f},"~S,~S,~N,~N,~B,~B");c$.isGap=d(c$,"isGap",function(a){return"-"==a||"."== +a||" "==a?!0:!1},"~S");c$.isNucleotide=d(c$,"isNucleotide",function(a){if(null==a)return!1;for(var b=0,c=0,f,l=0;l=d&&(d=String.fromCharCode(d.charCodeAt(0)-32)),"A"==d||"G"==d||"C"==d||"T"==d||"U"==d?b++:jalview.util.Comparison.isGap(d)||c++;return 100*b>85*(b+c)?!0:!1},"~A");c$.isNucleotide2=d(c$,"isNucleotide2",function(a){if(null==a)return!1;for(var b=new java.util.ArrayList,c,f=0;f< +a.length&&((c=a[f])||1);f++)for(var l,d=0,g=c;dl);do b+=1;while(a[b]l);do b+=1;while(a[b]a[c].compareTo(l));do b+=1;while(0f&&g.getDatasetSequence().getStart()=d&&(l.append(f),n=0);else{h[e++]=g+1;if(e==d){for(var e=new jalview.datamodel.SearchResults,q,s=0,r=h;sb.pos3&&a.pos1>=b.pos1)return 1;if(b.pos3>a.pos3&&b.pos1>=a.pos1)return-1;if(a.pos1==b.pos1&&a.pos3==b.pos3)return Integer.compare(a.pos2,b.pos2);var c=Integer.compare(a.pos2,b.pos2);return 0!=c?c:Integer.compare(a.pos1,b.pos1)},"jalview.datamodel.AlignedCodon,jalview.datamodel.AlignedCodon");p("jalview.datamodel");q(null,"jalview.datamodel.AlignedCodonFrame",["jalview.datamodel.Mapping","jalview.util.MappingUtils", +"java.util.ArrayList"],function(){c$=s(function(){this.dnaToProt=this.dnaSeqs=null;r(this,arguments)},jalview.datamodel,"AlignedCodonFrame");m(c$,function(){});d(c$,"addMap",function(a,b,c){var f=1;null!=this.dnaSeqs&&(f=this.dnaSeqs.length+1);var l=Array(f),d=Array(f);null!=this.dnaSeqs&&(System.arraycopy(this.dnaSeqs,0,l,0,this.dnaSeqs.length),System.arraycopy(this.dnaToProt,0,d,0,this.dnaSeqs.length));this.dnaSeqs=l;this.dnaToProt=d;f--;this.dnaSeqs[f]=null==a.getDatasetSequence()?a:a.getDatasetSequence(); +a=new jalview.datamodel.Mapping(c);a.to=null==b.getDatasetSequence()?b:b.getDatasetSequence();this.dnaToProt[f]=a},"jalview.datamodel.SequenceI,jalview.datamodel.SequenceI,jalview.util.MapList");d(c$,"getdnaSeqs",function(){return this.dnaSeqs});d(c$,"getAaSeqs",function(){if(null==this.dnaToProt)return null;for(var a=Array(this.dnaToProt.length),b=0;bb?b:this.map.getToHighest(),a>b)return null}else if(a=this.map.getToHighest()>a?a:this.map.getToHighest(),b=this.map.getToLowest()b?b:this.map.getFromHighest(),a>b)return null}else if(a=this.map.getFromHighest()>a?a:this.map.getFromHighest(),b=this.map.getFromLowest()=this.currentFromRange[1]?!1:!0});e(c$,"next",function(){if(!this.hasNext())throw new java.util.NoSuchElementException;var a=this.getNextCodon(),a=this.getAlignedCodon(a), +b=this.getPeptide();return new jalview.datamodel.AlignedCodon(a[0],a[1],a[2],b)});d(c$,"getPeptide",function(){if(this.toPosition<=this.currentToRange[1]){var a=this.b$["jalview.datamodel.Mapping"].to.getSequence()[this.toPosition-1];this.toPosition++;return String.valueOf(a)}if(!this.toRanges.hasNext())throw new java.util.NoSuchElementException("Ran out of peptide at position "+this.toPosition);this.currentToRange=this.toRanges.next();this.toPosition=this.currentToRange[0];return this.getPeptide()}); +d(c$,"getNextCodon",function(){for(var a=w(3,0),b=0;3>b;)if(this.fromPosition<=this.currentFromRange[1])a[b++]=this.fromPosition++;else{if(!this.fromRanges.hasNext())throw new jalview.datamodel.IncompleteCodonException;this.currentFromRange=this.fromRanges.next();this.fromPosition=this.currentFromRange[0]}return a});d(c$,"getAlignedCodon",function(a){for(var b=w(a.length,0),c=0;ca||3=d)return null;var g= +a.get(l++),h=g[0],e=g[1];h>e&&(h=g[1],e=g[0]);for(;le&&(e=g[0]),g[1]>e&&(e=g[1]);for(var d=l=0,g=w(e-h+2,0),n=0;nd&&(d=x[0])));g[n]=x}a=E(-1,[w(-1,[h,e,l,d]),w(e-h+2,0)]);a[0][2]=l;a[0][3]=d;for(n=0;n=f[0]&&b<=f[1])return w(-1,[c+b-f[0]+1,1]);c+=f[1]-f[0]+1}else{if(b>=f[1]&&b<=f[0])return w(-1,[c+f[0]-b+1,-1]);c+=f[0]-f[1]+1}return null},"java.util.List,~N");c$.countToPos=d(c$,"countToPos",function(a,b){for(var c=0,f=0,l=0,d=a.size(),g=w(-1,[0,0]);l=g[0]&&b<=g[1])&&(e=h),c>=g[0]&&c<=g[1]&&(-1==n&&(n=h),-1!=n&&(c+l<=g[1]?(x=h,c+=l):l-=g[1]-c))):(-1==e&&(b<=g[0]&&b>=g[1])&&(e=h),c<=g[0]&&c>=g[1]&&(-1==n&&(n=h),-1!=n&&(c-l>=g[1]?(x=h,c-=l):l-=c-g[1]))),h++;if(e==x&&-1==x)return null;l=new java.util.ArrayList;if(e<=x){h=f=e;g=a.get(f++);g=w(-1,[g[0],g[1]]);for(h==e&&(g[0]=b);h!=x;)l.add(g),g=a.get(f++),g=w(-1,[g[0],g[1]]),h++}else{for(h=a.size()-1;h>e;)h--;g=a.get(h);g=w(-1,[g[1],g[0]]);for(h==e&&(g[0]=b);--h!=x;)l.add(g), +g=a.get(h),g=w(-1,[g[1],g[0]])}h==x&&(g[1]=c);l.add(g);a=null;if(null!=l&&0=b.getFromLowest()&&this.getFromHighest()<=b.getFromHighest()||this.getFromLowest()<=b.getFromLowest()&&this.getFromHighest()>=b.getFromHighest():this.getToLowest()>= +b.getToLowest()&&this.getToHighest()<=b.getToHighest()||this.getToLowest()<=b.getToLowest()&&this.getToHighest()>=b.getToHighest()},"~B,jalview.util.MapList");e(c$,"toString",function(){var a=new StringBuilder(64);a.append("From (").append(this.fromRatio).append(":").append(this.toRatio).append(") [");for(var b,c=this.fromShifts.iterator();c.hasNext()&&((b=c.next())||1);)a.append(" ").append(java.util.Arrays.toString(b));a.append(" ] To [");for(c=this.toShifts.iterator();c.hasNext()&&((b=c.next())|| +1);)a.append(" ").append(java.util.Arrays.toString(b));a.append(" ]");return a.toString()})});p("jalview.util");q(null,"jalview.util.MappingUtils","jalview.analysis.AlignmentSorter jalview.commands.EditCommand $.OrderCommand jalview.datamodel.AlignmentOrder $.ColumnSelection $.SearchResults $.Sequence $.SequenceGroup jalview.util.Comparison $.StringUtils java.util.ArrayList $.Collections $.HashMap".split(" "),function(){c$=B(jalview.util,"MappingUtils");c$.mapCutOrPaste=d(c$,"mapCutOrPaste",function(a, +b){var c=a.getAction();b&&c.getUndoAction();System.err.println("MappingUtils.mapCutOrPaste not yet implemented")},"jalview.commands.EditCommand.Edit,~B,java.util.List,jalview.commands.EditCommand,java.util.Set");c$.mapEditCommand=d(c$,"mapEditCommand",function(a,b,c,f,l){if(!c.isNucleotide())return null;for(var d=new java.util.HashMap,g,h=c.getSequences().iterator();h.hasNext()&&((g=h.next())||1);){var e=g.getDatasetSequence();if(null!=e){var n=new jalview.datamodel.Sequence(g);n.setDatasetSequence(e); +d.put(e,n)}}g=a.priorState(b);h=new jalview.commands.EditCommand;for(a=a.getEditIterator(!b);a.hasNext();)e=a.next(),e.getAction()===jalview.commands.EditCommand.Action.CUT||e.getAction()===jalview.commands.EditCommand.Action.PASTE?jalview.util.MappingUtils.mapCutOrPaste(e,b,c.getSequences(),h,l):(e.getAction()===jalview.commands.EditCommand.Action.INSERT_GAP||e.getAction()===jalview.commands.EditCommand.Action.DELETE_GAP)&&jalview.util.MappingUtils.mapInsertOrDelete(e,b,g,c.getSequences(),d,f,h, +l);return 0=b.getStart()&&c<=b.getEnd()){var l;for(f=f.iterator();f.hasNext()&&((l=f.next())||1);)l.markMappedRegion(b,c,a)}},"jalview.datamodel.SearchResults,jalview.datamodel.SequenceI,~N,java.util.Set");c$.mapSequenceGroup=d(c$, +"mapSequenceGroup",function(a,b,c){var f=c.isNucleotide();b=(f?b:c).getAlignment().getCodonFrames();var l=new jalview.datamodel.SequenceGroup(a);l.cs=c.getGlobalColourScheme();l.clear();var d=-1,g=-1,h=a.getStartRes(),e=a.getEndRes(),n;for(a=a.getSequences().iterator();a.hasNext()&&((n=a.next())||1);){for(var x=h;x<=e&&jalview.util.Comparison.isGap(n.getCharAt(x));)x++;if(!(x>e)){for(var u=e;u>=h&&jalview.util.Comparison.isGap(n.getCharAt(u));)u--;for(var x=n.findPosition(x),u=n.findPosition(u),D, +m=b.iterator();m.hasNext()&&((D=m.next())||1);){var p=f?D.getDnaForAaSeq(n):D.getAaForDnaSeq(n);if(null!=p)for(var q,s=c.getAlignment().getSequences().iterator();s.hasNext()&&((q=s.next())||1);){var r=0,t=0;if(q.getDatasetSequence()===p){for(var p=jalview.util.MappingUtils.buildSearchResults(n,x,java.util.Collections.singleton(D)),v,p=p.getResults().iterator();p.hasNext()&&((v=p.next())||1);)r=v.getStart(),t=v.getEnd();p=jalview.util.MappingUtils.buildSearchResults(n,u,java.util.Collections.singleton(D)); +for(p=p.getResults().iterator();p.hasNext()&&((v=p.next())||1);)r=Math.min(r,v.getStart()),t=Math.max(t,v.getEnd());r=q.findIndex(r)-1;d=-1==d?r:Math.min(d,r);t=q.findIndex(t)-1;g=-1==g?t:Math.max(g,t);l.addSequence(q,!1);break}}}}}l.setStartRes(0>d?0:d);l.setEndRes(0>g?0:g);return l},"jalview.datamodel.SequenceGroup,jalview.api.AlignViewportI,jalview.api.AlignViewportI");c$.mapOrderCommand=d(c$,"mapOrderCommand",function(a,b,c,f){b=a.getSequenceOrder(b);for(var l=new java.util.ArrayList,d=0,g=c.isNucleotide(), +h,e=0;ea.position){a.string[f]=l.getSequence(a.position,a.position+a.number);var d=l.getDatasetSequence();null!=a.oldds&&null!=a.oldds[f]&&l.setDatasetSequence(null);l.deleteChars(a.position,a.position+a.number);if(null!=a.oldds&&null!=a.oldds[f])l.setDatasetSequence(a.oldds[f]),a.oldds[f]=d;else if(d!==l.getDatasetSequence()||null!=l.getSequenceFeatures())null==a.oldds&&(a.oldds=Array(a.seqs.length)),a.oldds[f]= +d,jalview.commands.EditCommand.adjustFeatures(a,f,l.findPosition(a.position),l.findPosition(a.position+a.number),!1)}1>l.getLength()&&(a.al.deleteSequence(l),c=!0)}jalview.commands.EditCommand.adjustAnnotations(a,!1,c,b)},"jalview.commands.EditCommand.Edit,~A");c$.paste=d(c$,"paste",function(a,b){for(var c,f,l,d,g,h=!1,e=0,n=0,x=0;xa.seqs[x].getLength()&&(a.alIndex[x]a.alIndex[x]||(void 0).add(a.alIndex[x],a.seqs[x]): +a.al.addSequence(a.seqs[x]),h=!0);d=a.seqs[x].getStart();g=a.seqs[x].getEnd();c=new StringBuffer;c.append(a.seqs[x].getSequence());if(null!=a.string&&null!=a.string[x]){if(a.position>=c.length())for(var u=a.position-c.length();0=d?d:d-a.number:d,0>f&&(f=d),c=Array(f);b?a.positiona.position?(f=Math.min(a.position,l[g].annotations.length),0=a.position&&(f=Math.min(a.number,l[g].annotations.length-a.position),0a.position+a.number&&System.arraycopy(l[g].annotations,a.position+a.number,c,a.position,l[g].annotations.length-a.position-a.number)):(c=d-a.position,0f?(l[e].setBegin(n.getBegin()-h),l[e].setEnd(n.getEnd()-h)):(l[e].getBegin()>=c&&l[e].setBegin(c),l[e].getEnd()< +f&&l[e].setEnd(f-1),l[e].setEnd(l[e].getEnd()-h),l[e].getBegin()>l[e].getEnd()&&d.deleteFeature(l[e])))}null==a.editedFeatures&&(a.editedFeatures=new java.util.Hashtable);a.editedFeatures.put(b,g)}},"jalview.commands.EditCommand.Edit,~N,~N,~N,~B");d(c$,"getEdits",function(){return this.edits});d(c$,"priorState",function(a){var b=new java.util.HashMap;if(null==this.getEdits())return b;if(a){for(var c,f=this.getEdits().iterator();f.hasNext()&&((c=f.next())||1);){var l;a=0;for(var d=c.getSequences();a< +d.length&&((l=d[a])||1);a++){var g=l.getDatasetSequence(),e=b.get(g);null==e&&(e=new jalview.datamodel.Sequence("",l.getSequenceAsString()),e.setDatasetSequence(g),b.put(g,e))}}return b}for(c=new jalview.util.ReverseListIterator(this.getEdits());c.hasNext();){var d=c.next(),f=d.getAction(),j=d.getPosition(),n=d.getNumber(),x=d.getGapCharacter();a=0;for(d=d.getSequences();aa&&(a=this.score[b][this.seq2.length-1],this.maxi=b,this.maxj= +this.seq2.length-1);for(var c=0;ca&&(a=this.score[this.seq1.length-1][c],this.maxi=this.seq1.length-1,this.maxj=c);b=this.maxi;c=this.maxj;this.maxscore=F(this.score[b][c]/10);this.seq1end=this.maxi+1;this.seq2end=this.maxj+1;this.aseq1=w(this.seq1.length+this.seq2.length,0);this.aseq2=w(this.seq1.length+this.seq2.length,0);for(this.count=this.seq1.length+this.seq2.length-1;0f&&(f=this.s2.getName().length);30f&&(b=this.s1.getName().substring(0,30)),this.s2.getName().length>f&&(c=this.s2.getName().substring(0,30)));var l=72-f-1,d=F((this.aseq1.length- +this.count)/l)+1;this.pid=0;this.output.append("Score = ").append(""+this.score[this.maxi][this.maxj]).append(jalview.analysis.AlignSeq.NEWLINE);this.output.append("Length of alignment = ").append(String.valueOf(this.aseq1.length-this.count)).append(jalview.analysis.AlignSeq.NEWLINE);this.output.append("Sequence ");this.output.append((new jalview.util.Format("%"+f+"s")).form(this.s1.getName()));this.output.append(" : ").append(String.valueOf(this.s1.getStart())).append(" - ").append(String.valueOf(this.s1.getEnd())); +this.output.append(" (Sequence length = ").append(String.valueOf(this.s1str.length)).append(")").append(jalview.analysis.AlignSeq.NEWLINE);this.output.append("Sequence ");this.output.append((new jalview.util.Format("%"+f+"s")).form(this.s2.getName()));this.output.append(" : ").append(String.valueOf(this.s2.getStart())).append(" - ").append(String.valueOf(this.s2.getEnd()));this.output.append(" (Sequence length = ").append(String.valueOf(this.s2str.length)).append(")").append(jalview.analysis.AlignSeq.NEWLINE).append(jalview.analysis.AlignSeq.NEWLINE); +for(var g=0;gf?(f=this.F[a][b],c=-1):this.F[a][b]==f&&-1==this.prev&&(f=this.F[a][b],c=-1);this.E[a][b]>=f?c=1:this.E[a][b]==f&&1==this.prev&&(c=1);return this.prev=c},"~N,~N");d(c$,"calcScoreMatrix", +function(){var a=this.seq1.length,b=this.seq2.length;this.score[0][0]=10*this.lookup[this.seq1[0]][this.seq2[0]];this.E[0][0]=-this.gapExtend;this.F[0][0]=0;for(var c=1;ca&&(f=b);c>f&&(f=c);return f},"~N,~N,~N");d(c$,"max",function(a,b){var c=a;b>a&&(c=b);return c},"~N,~N");d(c$,"stringToInt",function(a){for(var b=w(a.length,0),c=0;c=f&& +(f=String.fromCharCode(f.charCodeAt(0)-32));try{if(b[c]=this.charToInt[f.charCodeAt(0)],0>b[c]||b[c]>this.defInt)b[c]=this.defInt}catch(l){if(y(l,Exception))b[c]=this.defInt;else throw l;}}return b},"~S,~S");c$.displayMatrix=d(c$,"displayMatrix",function(a,b,c,f,l){for(var d=-1E3,g=1E3,e=0;e=d&&(d=b[e][j]),b[e][j]<=g&&(g=b[e][j]);System.out.println(d+" "+g);for(e=0;e +q)q=t.getMaxScore(),p=t,m=s}System.out.println("Best Score for "+(n.size()+1)+" :"+q);n.add(m);x.add(p);f.deleteSequence(m)}f=0;for(l=a.size();fl[e])j+=g.charAt(e),k[e]=N(-1,[g.charAt(e)]);else{var j=j+f[e][l[e]],n=jalview.schemes.ResidueProperties.ambiguityCodes.get(f[e][l[e]]);k[e]=N(n.length,"\x00");h=0;for(var x,u=0;u=k[e].length&&0=f[e].length&&0a;a++)jalview.schemes.ResidueProperties.aaIndex[a]= +23;jalview.schemes.ResidueProperties.aaIndex[65]=0;jalview.schemes.ResidueProperties.aaIndex[82]=1;jalview.schemes.ResidueProperties.aaIndex[78]=2;jalview.schemes.ResidueProperties.aaIndex[68]=3;jalview.schemes.ResidueProperties.aaIndex[67]=4;jalview.schemes.ResidueProperties.aaIndex[81]=5;jalview.schemes.ResidueProperties.aaIndex[69]=6;jalview.schemes.ResidueProperties.aaIndex[71]=7;jalview.schemes.ResidueProperties.aaIndex[72]=8;jalview.schemes.ResidueProperties.aaIndex[73]=9;jalview.schemes.ResidueProperties.aaIndex[76]= +10;jalview.schemes.ResidueProperties.aaIndex[75]=11;jalview.schemes.ResidueProperties.aaIndex[77]=12;jalview.schemes.ResidueProperties.aaIndex[70]=13;jalview.schemes.ResidueProperties.aaIndex[80]=14;jalview.schemes.ResidueProperties.aaIndex[83]=15;jalview.schemes.ResidueProperties.aaIndex[84]=16;jalview.schemes.ResidueProperties.aaIndex[87]=17;jalview.schemes.ResidueProperties.aaIndex[89]=18;jalview.schemes.ResidueProperties.aaIndex[86]=19;jalview.schemes.ResidueProperties.aaIndex[66]=20;jalview.schemes.ResidueProperties.aaIndex[90]= +21;jalview.schemes.ResidueProperties.aaIndex[88]=22;jalview.schemes.ResidueProperties.aaIndex[85]=22;jalview.schemes.ResidueProperties.aaIndex[97]=0;jalview.schemes.ResidueProperties.aaIndex[114]=1;jalview.schemes.ResidueProperties.aaIndex[110]=2;jalview.schemes.ResidueProperties.aaIndex[100]=3;jalview.schemes.ResidueProperties.aaIndex[99]=4;jalview.schemes.ResidueProperties.aaIndex[113]=5;jalview.schemes.ResidueProperties.aaIndex[101]=6;jalview.schemes.ResidueProperties.aaIndex[103]=7;jalview.schemes.ResidueProperties.aaIndex[104]= +8;jalview.schemes.ResidueProperties.aaIndex[105]=9;jalview.schemes.ResidueProperties.aaIndex[108]=10;jalview.schemes.ResidueProperties.aaIndex[107]=11;jalview.schemes.ResidueProperties.aaIndex[109]=12;jalview.schemes.ResidueProperties.aaIndex[102]=13;jalview.schemes.ResidueProperties.aaIndex[112]=14;jalview.schemes.ResidueProperties.aaIndex[115]=15;jalview.schemes.ResidueProperties.aaIndex[116]=16;jalview.schemes.ResidueProperties.aaIndex[119]=17;jalview.schemes.ResidueProperties.aaIndex[121]=18; +jalview.schemes.ResidueProperties.aaIndex[118]=19;jalview.schemes.ResidueProperties.aaIndex[98]=20;jalview.schemes.ResidueProperties.aaIndex[122]=21;jalview.schemes.ResidueProperties.aaIndex[120]=22;jalview.schemes.ResidueProperties.aaIndex[117]=22;G(c$,"maxProteinIndex",23,"maxNucleotideIndex",10);jalview.schemes.ResidueProperties.nucleotideIndex=w(255,0);for(a=0;255>a;a++)jalview.schemes.ResidueProperties.nucleotideIndex[a]=10;jalview.schemes.ResidueProperties.nucleotideIndex[65]=0;jalview.schemes.ResidueProperties.nucleotideIndex[97]= +0;jalview.schemes.ResidueProperties.nucleotideIndex[67]=1;jalview.schemes.ResidueProperties.nucleotideIndex[99]=1;jalview.schemes.ResidueProperties.nucleotideIndex[71]=2;jalview.schemes.ResidueProperties.nucleotideIndex[103]=2;jalview.schemes.ResidueProperties.nucleotideIndex[84]=3;jalview.schemes.ResidueProperties.nucleotideIndex[116]=3;jalview.schemes.ResidueProperties.nucleotideIndex[85]=4;jalview.schemes.ResidueProperties.nucleotideIndex[117]=4;jalview.schemes.ResidueProperties.nucleotideIndex[73]= +5;jalview.schemes.ResidueProperties.nucleotideIndex[105]=5;jalview.schemes.ResidueProperties.nucleotideIndex[88]=6;jalview.schemes.ResidueProperties.nucleotideIndex[120]=6;jalview.schemes.ResidueProperties.nucleotideIndex[82]=7;jalview.schemes.ResidueProperties.nucleotideIndex[114]=7;jalview.schemes.ResidueProperties.nucleotideIndex[89]=8;jalview.schemes.ResidueProperties.nucleotideIndex[121]=8;jalview.schemes.ResidueProperties.nucleotideIndex[78]=9;jalview.schemes.ResidueProperties.nucleotideIndex[110]= +9;jalview.schemes.ResidueProperties.nucleotideName.put("A","Adenine");jalview.schemes.ResidueProperties.nucleotideName.put("a","Adenine");jalview.schemes.ResidueProperties.nucleotideName.put("G","Guanine");jalview.schemes.ResidueProperties.nucleotideName.put("g","Guanine");jalview.schemes.ResidueProperties.nucleotideName.put("C","Cytosine");jalview.schemes.ResidueProperties.nucleotideName.put("c","Cytosine");jalview.schemes.ResidueProperties.nucleotideName.put("T","Thymine");jalview.schemes.ResidueProperties.nucleotideName.put("t", +"Thymine");jalview.schemes.ResidueProperties.nucleotideName.put("U","Uracil");jalview.schemes.ResidueProperties.nucleotideName.put("u","Uracil");jalview.schemes.ResidueProperties.nucleotideName.put("I","Inosine");jalview.schemes.ResidueProperties.nucleotideName.put("i","Inosine");jalview.schemes.ResidueProperties.nucleotideName.put("X","Xanthine");jalview.schemes.ResidueProperties.nucleotideName.put("x","Xanthine");jalview.schemes.ResidueProperties.nucleotideName.put("R","Unknown Purine");jalview.schemes.ResidueProperties.nucleotideName.put("r", +"Unknown Purine");jalview.schemes.ResidueProperties.nucleotideName.put("Y","Unknown Pyrimidine");jalview.schemes.ResidueProperties.nucleotideName.put("y","Unknown Pyrimidine");jalview.schemes.ResidueProperties.nucleotideName.put("N","Unknown");jalview.schemes.ResidueProperties.nucleotideName.put("n","Unknown");jalview.schemes.ResidueProperties.nucleotideName.put("W","Weak nucleotide (A or T)");jalview.schemes.ResidueProperties.nucleotideName.put("w","Weak nucleotide (A or T)");jalview.schemes.ResidueProperties.nucleotideName.put("S", +"Strong nucleotide (G or C)");jalview.schemes.ResidueProperties.nucleotideName.put("s","Strong nucleotide (G or C)");jalview.schemes.ResidueProperties.nucleotideName.put("M","Amino (A or C)");jalview.schemes.ResidueProperties.nucleotideName.put("m","Amino (A or C)");jalview.schemes.ResidueProperties.nucleotideName.put("K","Keto (G or T)");jalview.schemes.ResidueProperties.nucleotideName.put("k","Keto (G or T)");jalview.schemes.ResidueProperties.nucleotideName.put("B","Not A (G or C or T)");jalview.schemes.ResidueProperties.nucleotideName.put("b", +"Not A (G or C or T)");jalview.schemes.ResidueProperties.nucleotideName.put("H","Not G (A or C or T)");jalview.schemes.ResidueProperties.nucleotideName.put("h","Not G (A or C or T)");jalview.schemes.ResidueProperties.nucleotideName.put("D","Not C (A or G or T)");jalview.schemes.ResidueProperties.nucleotideName.put("d","Not C (A or G or T)");jalview.schemes.ResidueProperties.nucleotideName.put("V","Not T (A or G or C");jalview.schemes.ResidueProperties.nucleotideName.put("v","Not T (A or G or C"); +jalview.schemes.ResidueProperties.purinepyrimidineIndex=w(255,0);for(a=0;255>a;a++)jalview.schemes.ResidueProperties.purinepyrimidineIndex[a]=3;jalview.schemes.ResidueProperties.purinepyrimidineIndex[65]=0;jalview.schemes.ResidueProperties.purinepyrimidineIndex[97]=0;jalview.schemes.ResidueProperties.purinepyrimidineIndex[67]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[99]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[71]=0;jalview.schemes.ResidueProperties.purinepyrimidineIndex[103]= +0;jalview.schemes.ResidueProperties.purinepyrimidineIndex[84]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[116]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[85]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[117]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[73]=2;jalview.schemes.ResidueProperties.purinepyrimidineIndex[105]=2;jalview.schemes.ResidueProperties.purinepyrimidineIndex[88]=2;jalview.schemes.ResidueProperties.purinepyrimidineIndex[120]=2; +jalview.schemes.ResidueProperties.purinepyrimidineIndex[82]=0;jalview.schemes.ResidueProperties.purinepyrimidineIndex[114]=0;jalview.schemes.ResidueProperties.purinepyrimidineIndex[89]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[121]=1;jalview.schemes.ResidueProperties.purinepyrimidineIndex[78]=2;jalview.schemes.ResidueProperties.purinepyrimidineIndex[110]=2;jalview.schemes.ResidueProperties.aa3Hash.put("ALA",new Integer(0));jalview.schemes.ResidueProperties.aa3Hash.put("ARG",new Integer(1)); +jalview.schemes.ResidueProperties.aa3Hash.put("ASN",new Integer(2));jalview.schemes.ResidueProperties.aa3Hash.put("ASP",new Integer(3));jalview.schemes.ResidueProperties.aa3Hash.put("CYS",new Integer(4));jalview.schemes.ResidueProperties.aa3Hash.put("GLN",new Integer(5));jalview.schemes.ResidueProperties.aa3Hash.put("GLU",new Integer(6));jalview.schemes.ResidueProperties.aa3Hash.put("GLY",new Integer(7));jalview.schemes.ResidueProperties.aa3Hash.put("HIS",new Integer(8));jalview.schemes.ResidueProperties.aa3Hash.put("ILE", +new Integer(9));jalview.schemes.ResidueProperties.aa3Hash.put("LEU",new Integer(10));jalview.schemes.ResidueProperties.aa3Hash.put("LYS",new Integer(11));jalview.schemes.ResidueProperties.aa3Hash.put("MET",new Integer(12));jalview.schemes.ResidueProperties.aa3Hash.put("PHE",new Integer(13));jalview.schemes.ResidueProperties.aa3Hash.put("PRO",new Integer(14));jalview.schemes.ResidueProperties.aa3Hash.put("SER",new Integer(15));jalview.schemes.ResidueProperties.aa3Hash.put("THR",new Integer(16));jalview.schemes.ResidueProperties.aa3Hash.put("TRP", +new Integer(17));jalview.schemes.ResidueProperties.aa3Hash.put("TYR",new Integer(18));jalview.schemes.ResidueProperties.aa3Hash.put("VAL",new Integer(19));jalview.schemes.ResidueProperties.aa3Hash.put("ASX",new Integer(20));jalview.schemes.ResidueProperties.aa3Hash.put("GLX",new Integer(21));jalview.schemes.ResidueProperties.aa3Hash.put("XAA",new Integer(22));jalview.schemes.ResidueProperties.aa3Hash.put("-",new Integer(23));jalview.schemes.ResidueProperties.aa3Hash.put("*",new Integer(23));jalview.schemes.ResidueProperties.aa3Hash.put(".", +new Integer(23));jalview.schemes.ResidueProperties.aa3Hash.put(" ",new Integer(23));jalview.schemes.ResidueProperties.aa3Hash.put("Gap",new Integer(23));jalview.schemes.ResidueProperties.aa2Triplet.put("A","ALA");jalview.schemes.ResidueProperties.aa2Triplet.put("a","ALA");jalview.schemes.ResidueProperties.aa2Triplet.put("R","ARG");jalview.schemes.ResidueProperties.aa2Triplet.put("r","ARG");jalview.schemes.ResidueProperties.aa2Triplet.put("N","ASN");jalview.schemes.ResidueProperties.aa2Triplet.put("n", +"ASN");jalview.schemes.ResidueProperties.aa2Triplet.put("D","ASP");jalview.schemes.ResidueProperties.aa2Triplet.put("d","ASP");jalview.schemes.ResidueProperties.aa2Triplet.put("C","CYS");jalview.schemes.ResidueProperties.aa2Triplet.put("c","CYS");jalview.schemes.ResidueProperties.aa2Triplet.put("Q","GLN");jalview.schemes.ResidueProperties.aa2Triplet.put("q","GLN");jalview.schemes.ResidueProperties.aa2Triplet.put("E","GLU");jalview.schemes.ResidueProperties.aa2Triplet.put("e","GLU");jalview.schemes.ResidueProperties.aa2Triplet.put("G", +"GLY");jalview.schemes.ResidueProperties.aa2Triplet.put("g","GLY");jalview.schemes.ResidueProperties.aa2Triplet.put("H","HIS");jalview.schemes.ResidueProperties.aa2Triplet.put("h","HIS");jalview.schemes.ResidueProperties.aa2Triplet.put("I","ILE");jalview.schemes.ResidueProperties.aa2Triplet.put("i","ILE");jalview.schemes.ResidueProperties.aa2Triplet.put("L","LEU");jalview.schemes.ResidueProperties.aa2Triplet.put("l","LEU");jalview.schemes.ResidueProperties.aa2Triplet.put("K","LYS");jalview.schemes.ResidueProperties.aa2Triplet.put("k", +"LYS");jalview.schemes.ResidueProperties.aa2Triplet.put("M","MET");jalview.schemes.ResidueProperties.aa2Triplet.put("m","MET");jalview.schemes.ResidueProperties.aa2Triplet.put("F","PHE");jalview.schemes.ResidueProperties.aa2Triplet.put("f","PHE");jalview.schemes.ResidueProperties.aa2Triplet.put("P","PRO");jalview.schemes.ResidueProperties.aa2Triplet.put("p","PRO");jalview.schemes.ResidueProperties.aa2Triplet.put("S","SER");jalview.schemes.ResidueProperties.aa2Triplet.put("s","SER");jalview.schemes.ResidueProperties.aa2Triplet.put("T", +"THR");jalview.schemes.ResidueProperties.aa2Triplet.put("t","THR");jalview.schemes.ResidueProperties.aa2Triplet.put("W","TRP");jalview.schemes.ResidueProperties.aa2Triplet.put("w","TRP");jalview.schemes.ResidueProperties.aa2Triplet.put("Y","TYR");jalview.schemes.ResidueProperties.aa2Triplet.put("y","TYR");jalview.schemes.ResidueProperties.aa2Triplet.put("V","VAL");jalview.schemes.ResidueProperties.aa2Triplet.put("v","VAL");G(c$,"aa",E(-1,"ARNDCQEGHILKMFPSTWYVBZX_*. ".split("")));c$.midBlue=c$.prototype.midBlue= +new java.awt.Color(100,100,255);c$.scaleColours=c$.prototype.scaleColours=new java.util.Vector;jalview.schemes.ResidueProperties.scaleColours.addElement(new java.awt.Color(114,0,147));jalview.schemes.ResidueProperties.scaleColours.addElement(new java.awt.Color(156,0,98));jalview.schemes.ResidueProperties.scaleColours.addElement(new java.awt.Color(190,0,0));jalview.schemes.ResidueProperties.scaleColours.addElement(java.awt.Color.red);jalview.schemes.ResidueProperties.scaleColours.addElement(new java.awt.Color(255, +125,0));jalview.schemes.ResidueProperties.scaleColours.addElement(java.awt.Color.orange);jalview.schemes.ResidueProperties.scaleColours.addElement(new java.awt.Color(255,194,85));jalview.schemes.ResidueProperties.scaleColours.addElement(java.awt.Color.yellow);jalview.schemes.ResidueProperties.scaleColours.addElement(new java.awt.Color(255,255,181));jalview.schemes.ResidueProperties.scaleColours.addElement(java.awt.Color.white);c$.taylor=c$.prototype.taylor=E(-1,[new java.awt.Color(204,255,0),new java.awt.Color(0, +0,255),new java.awt.Color(204,0,255),new java.awt.Color(255,0,0),new java.awt.Color(255,255,0),new java.awt.Color(255,0,204),new java.awt.Color(255,0,102),new java.awt.Color(255,153,0),new java.awt.Color(0,102,255),new java.awt.Color(102,255,0),new java.awt.Color(51,255,0),new java.awt.Color(102,0,255),new java.awt.Color(0,255,0),new java.awt.Color(0,255,102),new java.awt.Color(255,204,0),new java.awt.Color(255,51,0),new java.awt.Color(255,102,0),new java.awt.Color(0,204,255),new java.awt.Color(0, +255,204),new java.awt.Color(153,255,0),java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white]);c$.nucleotide=c$.prototype.nucleotide=E(-1,[new java.awt.Color(100,247,63),new java.awt.Color(255,179,64),new java.awt.Color(235,65,60),new java.awt.Color(60,136,238),new java.awt.Color(60,136,238),java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white]);c$.purinepyrimidine= +c$.prototype.purinepyrimidine=E(-1,[new java.awt.Color(255,131,250),new java.awt.Color(64,224,208),java.awt.Color.white,java.awt.Color.white]);c$.zappo=c$.prototype.zappo=E(-1,[java.awt.Color.pink,jalview.schemes.ResidueProperties.midBlue,java.awt.Color.green,java.awt.Color.red,java.awt.Color.yellow,java.awt.Color.green,java.awt.Color.red,java.awt.Color.magenta,jalview.schemes.ResidueProperties.midBlue,java.awt.Color.pink,java.awt.Color.pink,jalview.schemes.ResidueProperties.midBlue,java.awt.Color.pink, +java.awt.Color.orange,java.awt.Color.magenta,java.awt.Color.green,java.awt.Color.green,java.awt.Color.orange,java.awt.Color.orange,java.awt.Color.pink,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white,java.awt.Color.white]);G(c$,"hyd2",U(-1,[0.62,0.29,-0.9,-0.74,1.19,0.48,-0.4,1.38,-1.5,1.06,0.64,-0.78,0.12,-0.85,-2.53,-0.18,-0.05,1.08,0.81,0,0.26,0,0]),"helix",U(-1,[1.42,0.98,0.67,1.01,0.7,1.11,1.51,0.57,1,1.08,1.21,1.16, +1.45,1.13,0.57,0.77,0.83,1.08,0.69,1.06,0.84,1.31,1,0]),"helixmin",0.57,"helixmax",1.51,"strand",U(-1,[0.83,0.93,0.89,0.54,1.19,1.1,0.37,0.75,0.87,1.6,1.3,0.74,1.05,1.38,0.55,0.75,1.19,1.37,1.47,1.7,0.72,0.74,1,0]),"strandmin",0.37,"strandmax",1.7,"turn",U(-1,[0.66,0.95,1.56,1.46,1.19,0.98,0.74,1.56,0.95,0.47,0.59,1.01,0.6,0.6,1.52,1.43,0.96,0.96,1.14,0.5,1.51,0.86,1,0,0]),"turnmin",0.47,"turnmax",1.56,"buried",U(-1,[1.7,0.1,0.4,0.4,4.6,0.3,0.3,1.8,0.8,3.1,2.4,0.05,1.9,2.2,0.6,0.8,0.7,1.6,0.5,2.9, +0.4,0.3,1.358,0]),"buriedmin",0.05,"buriedmax",4.6,"hyd",U(-1,[1.8,-4.5,-3.5,-3.5,2.5,-3.5,-3.5,-0.4,-3.2,4.5,3.8,-3.9,1.9,2.8,-1.6,-0.8,-0.7,-0.9,-1.3,4.2,-3.5,-3.5,-0.49,0]),"hydmax",4.5,"hydmin",-3.9,"BLOSUM62",E(-1,[w(-1,[4,-1,-2,-2,0,-1,-1,0,-2,-1,-1,-1,-1,-2,-1,1,0,-3,-2,0,-2,-1,0,-4]),w(-1,[-1,5,0,-2,-3,1,0,-2,0,-3,-2,2,-1,-3,-2,-1,-1,-3,-2,-3,-1,0,-1,-4]),w(-1,[-2,0,6,1,-3,0,0,0,1,-3,-3,0,-2,-3,-2,1,0,-4,-2,-3,3,0,-1,-4]),w(-1,[-2,-2,1,6,-3,0,2,-1,-1,-3,-4,-1,-3,-3,-1,0,-1,-4,-3,-3,4,1,-1, +-4]),w(-1,[0,3,-3,-3,9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-3,-3,-2,-4]),w(-1,[-1,1,0,0,-3,5,2,-2,0,-3,-2,1,0,-3,-1,0,-1,-2,-1,-2,0,3,-1,-4]),w(-1,[-1,0,0,2,-4,2,5,-2,0,-3,-3,1,-2,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4]),w(-1,[0,-2,0,-1,-3,-2,-2,6,-2,-4,-4,-2,-3,-3,-2,0,-2,-2,-3,-3,-1,-2,-1,-4]),w(-1,[-2,0,1,-1,-3,0,0,-2,8,-3,-3,-1,-2,-1,-2,-1,-2,-2,2,-3,0,0,-1,-4]),w(-1,[-1,-3,-3,-3,-1,-3,-3,-4,-3,4,2,-3,1,0,-3,-2,-1,-3,-1,3,-3,-3,-1,-4]),w(-1,[-1,-2,-3,-4,-1,-2,-3,-4,-3,2,4,-2,2,0,-3,-2,-1,-2,-1, +1,-4,-3,-1,-4]),w(-1,[-1,2,0,-1,-3,1,1,-2,-1,-3,-2,5,-1,-3,-1,0,-1,-3,-2,-2,0,1,-1,-4]),w(-1,[-1,-1,-2,-3,-1,0,-2,-3,-2,1,2,-1,5,0,-2,-1,-1,-1,-1,1,-3,-1,-1,-4]),w(-1,[-2,-3,-3,-3,-2,-3,-3,-3,-1,0,0,-3,0,6,-4,-2,-2,1,3,-1,-3,-3,-1,-4]),w(-1,[-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4,7,-1,-1,-4,-3,-2,-2,-1,-2,-4]),w(-1,[1,-1,1,0,-1,0,0,0,-1,-2,-2,0,-1,-2,-1,4,1,-3,-2,-2,0,0,0,-4]),w(-1,[0,-1,0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1,1,5,-2,-2,0,-1,-1,0,-4]),w(-1,[-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1, +1,-4,-3,-2,11,2,-3,-4,-3,-2,-4]),w(-1,[-2,-2,-2,-3,-2,-1,-2,-3,2,-1,-1,-2,-1,3,-3,-2,-2,2,7,-1,-3,-2,-1,-4]),w(-1,[0,-3,-3,-3,-1,-2,-2,-3,-3,3,1,-2,1,-1,-2,-2,0,-3,-1,4,-3,-2,-1,-4]),w(-1,[-2,-1,3,4,-3,0,1,-1,0,-3,-4,0,-3,-3,-2,0,-1,-4,-3,-3,4,1,-1,-4]),w(-1,[-1,0,0,1,-3,3,4,-2,0,-3,-3,1,-1,-3,-1,0,-1,-3,-2,-2,1,4,-1,-4]),w(-1,[0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2,0,0,-2,-1,-1,-1,-1,-1,-4]),w(-1,[-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,1])]),"PAM250",E(-1,[w(-1, +[2,-2,0,0,-2,0,0,1,-1,-1,-2,-1,-1,-3,1,1,1,-6,-3,0,0,0,0,-8]),w(-1,[-2,6,0,-1,-4,1,-1,-3,2,-2,-3,3,0,-4,0,0,-1,2,-4,-2,-1,0,-1,-8]),w(-1,[0,0,2,2,-4,1,1,0,2,-2,-3,1,-2,-3,0,1,0,-4,-2,-2,2,1,0,-8]),w(-1,[0,-1,2,4,-5,2,3,1,1,-2,-4,0,-3,-6,-1,0,0,-7,-4,-2,3,3,-1,-8]),w(-1,[-2,-4,-4,-5,12,-5,-5,-3,-3,-2,-6,-5,-5,-4,-3,0,-2,-8,0,-2,-4,-5,-3,-8]),w(-1,[0,1,1,2,-5,4,2,-1,3,-2,-2,1,-1,-5,0,-1,-1,-5,-4,-2,1,3,-1,-8]),w(-1,[0,-1,1,3,-5,2,4,0,1,-2,-3,0,-2,-5,-1,0,0,-7,-4,-2,3,3,-1,-8]),w(-1,[1,-3,0,1,-3,-1, +0,5,-2,-3,-4,-2,-3,-5,0,1,0,-7,-5,-1,0,0,-1,-8]),w(-1,[-1,2,2,1,-3,3,1,-2,6,-2,-2,0,-2,-2,0,-1,-1,-3,0,-2,1,2,-1,-8]),w(-1,[-1,-2,-2,-2,-2,-2,-2,-3,-2,5,2,-2,2,1,-2,-1,0,-5,-1,4,-2,-2,-1,-8]),w(-1,[-2,-3,-3,-4,-6,-2,-3,-4,-2,2,6,-3,4,2,-3,-3,-2,-2,-1,2,-3,-3,-1,-8]),w(-1,[-1,3,1,0,-5,1,0,-2,0,-2,-3,5,0,-5,-1,0,0,-3,-4,-2,1,0,-1,-8]),w(-1,[-1,0,-2,-3,-5,-1,-2,-3,-2,2,4,0,6,0,-2,-2,-1,-4,-2,2,-2,-2,-1,-8]),w(-1,[-3,-4,-3,-6,-4,-5,-5,-5,-2,1,2,-5,0,9,-5,-3,-3,0,7,-1,-4,-5,-2,-8]),w(-1,[1,0,0,-1,-3,0, +-1,0,0,-2,-3,-1,-2,-5,6,1,0,-6,-5,-1,-1,0,-1,-8]),w(-1,[1,0,1,0,0,-1,0,1,-1,-1,-3,0,-2,-3,1,2,1,-2,-3,-1,0,0,0,-8]),w(-1,[1,-1,0,0,-2,-1,0,0,-1,0,-2,0,-1,-3,0,1,3,-5,-3,0,0,-1,0,-8]),w(-1,[-6,2,-4,-7,-8,-5,-7,-7,-3,-5,-2,-3,-4,0,-6,-2,-5,17,0,-6,-5,-6,-4,-8]),w(-1,[-3,-4,-2,-4,0,-4,-4,-5,0,-1,-1,-4,-2,7,-5,-3,-3,0,10,-2,-3,-4,-2,-8]),w(-1,[0,-2,-2,-2,-2,-2,-2,-1,-2,4,2,-2,2,-1,-1,-1,0,-6,-2,4,-2,-2,-1,-8]),w(-1,[0,-1,2,3,-4,1,3,0,1,-2,-3,1,-2,-4,-1,0,0,-5,-3,-2,3,2,-1,-8]),w(-1,[0,0,1,3,-5,3,3,0, +2,-2,-3,0,-2,-5,0,0,-1,-6,-4,-2,2,3,-1,-8]),w(-1,[0,-1,0,-1,-3,-1,-1,-1,-1,-1,-1,-1,-1,-2,-1,0,0,-4,-2,-1,-1,-1,-1,-8]),w(-1,[-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,-8,1])]));c$.ssHash=c$.prototype.ssHash=new java.util.Hashtable;jalview.schemes.ResidueProperties.ssHash.put("H",java.awt.Color.magenta);jalview.schemes.ResidueProperties.ssHash.put("E",java.awt.Color.yellow);jalview.schemes.ResidueProperties.ssHash.put("-",java.awt.Color.white);jalview.schemes.ResidueProperties.ssHash.put(".", +java.awt.Color.white);jalview.schemes.ResidueProperties.ssHash.put("S",java.awt.Color.cyan);jalview.schemes.ResidueProperties.ssHash.put("T",java.awt.Color.blue);jalview.schemes.ResidueProperties.ssHash.put("G",java.awt.Color.pink);jalview.schemes.ResidueProperties.ssHash.put("I",java.awt.Color.pink);jalview.schemes.ResidueProperties.ssHash.put("B",java.awt.Color.yellow);G(c$,"DNA",E(-1,[w(-1,[10,-8,-8,-8,-8,1,1,1,-8,1,1]),w(-1,[-8,10,-8,-8,-8,1,1,-8,1,1,1]),w(-1,[-8,-8,10,-8,-8,1,1,1,-8,1,1]),w(-1, +[-8,-8,-8,10,10,1,1,-8,1,1,1]),w(-1,[-8,-8,-8,10,10,1,1,-8,1,1,1]),w(-1,[1,1,1,1,1,10,0,0,0,1,1]),w(-1,[1,1,1,1,1,0,10,0,0,1,1]),w(-1,[1,-8,1,-8,-8,0,0,10,-8,1,1]),w(-1,[-8,1,-8,1,1,0,0,-8,10,1,1]),w(-1,[1,1,1,1,1,1,1,1,1,10,1]),w(-1,[1,1,1,1,1,1,1,1,1,1,1])]));jalview.schemes.ResidueProperties.scoreMatrices.put("BLOSUM62",new jalview.schemes.ScoreMatrix("BLOSUM62",jalview.schemes.ResidueProperties.BLOSUM62,0));jalview.schemes.ResidueProperties.scoreMatrices.put("PAM250",new jalview.schemes.ScoreMatrix("PAM250", +jalview.schemes.ResidueProperties.PAM250,0));jalview.schemes.ResidueProperties.scoreMatrices.put("DNA",new jalview.schemes.ScoreMatrix("DNA",jalview.schemes.ResidueProperties.DNA,1));c$.pidColours=c$.prototype.pidColours=E(-1,[jalview.schemes.ResidueProperties.midBlue,new java.awt.Color(153,153,255),new java.awt.Color(204,204,255)]);G(c$,"pidThresholds",Q(-1,[80,60,40]));c$.codonHash=c$.prototype.codonHash=new java.util.HashMap;c$.Lys=c$.prototype.Lys=new java.util.ArrayList;c$.Asn=c$.prototype.Asn= +new java.util.ArrayList;c$.Gln=c$.prototype.Gln=new java.util.ArrayList;c$.His=c$.prototype.His=new java.util.ArrayList;c$.Glu=c$.prototype.Glu=new java.util.ArrayList;c$.Asp=c$.prototype.Asp=new java.util.ArrayList;c$.Tyr=c$.prototype.Tyr=new java.util.ArrayList;c$.Thr=c$.prototype.Thr=new java.util.ArrayList;c$.Pro=c$.prototype.Pro=new java.util.ArrayList;c$.Ala=c$.prototype.Ala=new java.util.ArrayList;c$.Ser=c$.prototype.Ser=new java.util.ArrayList;c$.Arg=c$.prototype.Arg=new java.util.ArrayList; +c$.Gly=c$.prototype.Gly=new java.util.ArrayList;c$.Trp=c$.prototype.Trp=new java.util.ArrayList;c$.Cys=c$.prototype.Cys=new java.util.ArrayList;c$.Ile=c$.prototype.Ile=new java.util.ArrayList;c$.Met=c$.prototype.Met=new java.util.ArrayList;c$.Leu=c$.prototype.Leu=new java.util.ArrayList;c$.Val=c$.prototype.Val=new java.util.ArrayList;c$.Phe=c$.prototype.Phe=new java.util.ArrayList;c$.STOP=c$.prototype.STOP=new java.util.ArrayList;G(c$,"START","ATG");jalview.schemes.ResidueProperties.codonHash.put("K", +jalview.schemes.ResidueProperties.Lys);jalview.schemes.ResidueProperties.codonHash.put("N",jalview.schemes.ResidueProperties.Asn);jalview.schemes.ResidueProperties.codonHash.put("Q",jalview.schemes.ResidueProperties.Gln);jalview.schemes.ResidueProperties.codonHash.put("H",jalview.schemes.ResidueProperties.His);jalview.schemes.ResidueProperties.codonHash.put("E",jalview.schemes.ResidueProperties.Glu);jalview.schemes.ResidueProperties.codonHash.put("D",jalview.schemes.ResidueProperties.Asp);jalview.schemes.ResidueProperties.codonHash.put("Y", +jalview.schemes.ResidueProperties.Tyr);jalview.schemes.ResidueProperties.codonHash.put("T",jalview.schemes.ResidueProperties.Thr);jalview.schemes.ResidueProperties.codonHash.put("P",jalview.schemes.ResidueProperties.Pro);jalview.schemes.ResidueProperties.codonHash.put("A",jalview.schemes.ResidueProperties.Ala);jalview.schemes.ResidueProperties.codonHash.put("S",jalview.schemes.ResidueProperties.Ser);jalview.schemes.ResidueProperties.codonHash.put("R",jalview.schemes.ResidueProperties.Arg);jalview.schemes.ResidueProperties.codonHash.put("G", +jalview.schemes.ResidueProperties.Gly);jalview.schemes.ResidueProperties.codonHash.put("W",jalview.schemes.ResidueProperties.Trp);jalview.schemes.ResidueProperties.codonHash.put("C",jalview.schemes.ResidueProperties.Cys);jalview.schemes.ResidueProperties.codonHash.put("I",jalview.schemes.ResidueProperties.Ile);jalview.schemes.ResidueProperties.codonHash.put("M",jalview.schemes.ResidueProperties.Met);jalview.schemes.ResidueProperties.codonHash.put("L",jalview.schemes.ResidueProperties.Leu);jalview.schemes.ResidueProperties.codonHash.put("V", +jalview.schemes.ResidueProperties.Val);jalview.schemes.ResidueProperties.codonHash.put("F",jalview.schemes.ResidueProperties.Phe);jalview.schemes.ResidueProperties.codonHash.put("STOP",jalview.schemes.ResidueProperties.STOP);c$.ambiguityCodes=c$.prototype.ambiguityCodes=new java.util.Hashtable;c$.codonHash2=c$.prototype.codonHash2=new java.util.Hashtable;c$._ambiguityCodes=c$.prototype._ambiguityCodes=new java.util.Hashtable;jalview.schemes.ResidueProperties.ambiguityCodes.put("R",E(-1,["A","G"])); +jalview.schemes.ResidueProperties.ambiguityCodes.put("Y",E(-1,["T","C"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("W",E(-1,["A","T"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("S",E(-1,["G","C"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("M",E(-1,["A","C"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("K",E(-1,["G","T"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("H",E(-1,["A","T","C"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("B", +E(-1,["G","T","C"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("V",E(-1,["G","A","C"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("D",E(-1,["G","A","T"]));jalview.schemes.ResidueProperties.ambiguityCodes.put("N",E(-1,["G","A","T","C"]));jalview.schemes.ResidueProperties.codonHash2.put("AAA","K");jalview.schemes.ResidueProperties.codonHash2.put("AAG","K");jalview.schemes.ResidueProperties.codonHash2.put("AAC","N");jalview.schemes.ResidueProperties.codonHash2.put("AAT","N");jalview.schemes.ResidueProperties.codonHash2.put("CAA", +"Q");jalview.schemes.ResidueProperties.codonHash2.put("CAG","Q");jalview.schemes.ResidueProperties.codonHash2.put("CAC","H");jalview.schemes.ResidueProperties.codonHash2.put("CAT","H");jalview.schemes.ResidueProperties.codonHash2.put("GAA","E");jalview.schemes.ResidueProperties.codonHash2.put("GAG","E");jalview.schemes.ResidueProperties.codonHash2.put("GAC","D");jalview.schemes.ResidueProperties.codonHash2.put("GAT","D");jalview.schemes.ResidueProperties.codonHash2.put("TAC","Y");jalview.schemes.ResidueProperties.codonHash2.put("TAT", +"Y");jalview.schemes.ResidueProperties.codonHash2.put("ACA","T");jalview.schemes.ResidueProperties.codonHash2.put("ACC","T");jalview.schemes.ResidueProperties.codonHash2.put("ACT","T");jalview.schemes.ResidueProperties.codonHash2.put("ACG","T");jalview.schemes.ResidueProperties.codonHash2.put("CCA","P");jalview.schemes.ResidueProperties.codonHash2.put("CCG","P");jalview.schemes.ResidueProperties.codonHash2.put("CCC","P");jalview.schemes.ResidueProperties.codonHash2.put("CCT","P");jalview.schemes.ResidueProperties.codonHash2.put("GCA", +"A");jalview.schemes.ResidueProperties.codonHash2.put("GCG","A");jalview.schemes.ResidueProperties.codonHash2.put("GCC","A");jalview.schemes.ResidueProperties.codonHash2.put("GCT","A");jalview.schemes.ResidueProperties.codonHash2.put("TCA","S");jalview.schemes.ResidueProperties.codonHash2.put("TCG","S");jalview.schemes.ResidueProperties.codonHash2.put("TCC","S");jalview.schemes.ResidueProperties.codonHash2.put("TCT","S");jalview.schemes.ResidueProperties.codonHash2.put("AGC","S");jalview.schemes.ResidueProperties.codonHash2.put("AGT", +"S");jalview.schemes.ResidueProperties.codonHash2.put("AGA","R");jalview.schemes.ResidueProperties.codonHash2.put("AGG","R");jalview.schemes.ResidueProperties.codonHash2.put("CGA","R");jalview.schemes.ResidueProperties.codonHash2.put("CGG","R");jalview.schemes.ResidueProperties.codonHash2.put("CGC","R");jalview.schemes.ResidueProperties.codonHash2.put("CGT","R");jalview.schemes.ResidueProperties.codonHash2.put("GGA","G");jalview.schemes.ResidueProperties.codonHash2.put("GGG","G");jalview.schemes.ResidueProperties.codonHash2.put("GGC", +"G");jalview.schemes.ResidueProperties.codonHash2.put("GGT","G");jalview.schemes.ResidueProperties.codonHash2.put("TGA","*");jalview.schemes.ResidueProperties.codonHash2.put("TAA","*");jalview.schemes.ResidueProperties.codonHash2.put("TAG","*");jalview.schemes.ResidueProperties.codonHash2.put("TGG","W");jalview.schemes.ResidueProperties.codonHash2.put("TGC","C");jalview.schemes.ResidueProperties.codonHash2.put("TGT","C");jalview.schemes.ResidueProperties.codonHash2.put("ATA","I");jalview.schemes.ResidueProperties.codonHash2.put("ATC", +"I");jalview.schemes.ResidueProperties.codonHash2.put("ATT","I");jalview.schemes.ResidueProperties.codonHash2.put("ATG","M");jalview.schemes.ResidueProperties.codonHash2.put("CTA","L");jalview.schemes.ResidueProperties.codonHash2.put("CTG","L");jalview.schemes.ResidueProperties.codonHash2.put("CTC","L");jalview.schemes.ResidueProperties.codonHash2.put("CTT","L");jalview.schemes.ResidueProperties.codonHash2.put("TTA","L");jalview.schemes.ResidueProperties.codonHash2.put("TTG","L");jalview.schemes.ResidueProperties.codonHash2.put("GTA", +"V");jalview.schemes.ResidueProperties.codonHash2.put("GTG","V");jalview.schemes.ResidueProperties.codonHash2.put("GTC","V");jalview.schemes.ResidueProperties.codonHash2.put("GTT","V");jalview.schemes.ResidueProperties.codonHash2.put("TTC","F");jalview.schemes.ResidueProperties.codonHash2.put("TTT","F");jalview.schemes.ResidueProperties.buildAmbiguityCodonSet();jalview.schemes.ResidueProperties.Lys.add("AAA");jalview.schemes.ResidueProperties.Lys.add("AAG");jalview.schemes.ResidueProperties.Asn.add("AAC"); +jalview.schemes.ResidueProperties.Asn.add("AAT");jalview.schemes.ResidueProperties.Gln.add("CAA");jalview.schemes.ResidueProperties.Gln.add("CAG");jalview.schemes.ResidueProperties.His.add("CAC");jalview.schemes.ResidueProperties.His.add("CAT");jalview.schemes.ResidueProperties.Glu.add("GAA");jalview.schemes.ResidueProperties.Glu.add("GAG");jalview.schemes.ResidueProperties.Asp.add("GAC");jalview.schemes.ResidueProperties.Asp.add("GAT");jalview.schemes.ResidueProperties.Tyr.add("TAC");jalview.schemes.ResidueProperties.Tyr.add("TAT"); +jalview.schemes.ResidueProperties.Thr.add("ACA");jalview.schemes.ResidueProperties.Thr.add("ACG");jalview.schemes.ResidueProperties.Thr.add("ACC");jalview.schemes.ResidueProperties.Thr.add("ACT");jalview.schemes.ResidueProperties.Pro.add("CCA");jalview.schemes.ResidueProperties.Pro.add("CCG");jalview.schemes.ResidueProperties.Pro.add("CCC");jalview.schemes.ResidueProperties.Pro.add("CCT");jalview.schemes.ResidueProperties.Ala.add("GCA");jalview.schemes.ResidueProperties.Ala.add("GCG");jalview.schemes.ResidueProperties.Ala.add("GCC"); +jalview.schemes.ResidueProperties.Ala.add("GCT");jalview.schemes.ResidueProperties.Ser.add("TCA");jalview.schemes.ResidueProperties.Ser.add("TCG");jalview.schemes.ResidueProperties.Ser.add("TCC");jalview.schemes.ResidueProperties.Ser.add("TCT");jalview.schemes.ResidueProperties.Ser.add("AGC");jalview.schemes.ResidueProperties.Ser.add("AGT");jalview.schemes.ResidueProperties.Arg.add("AGA");jalview.schemes.ResidueProperties.Arg.add("AGG");jalview.schemes.ResidueProperties.Arg.add("CGA");jalview.schemes.ResidueProperties.Arg.add("CGG"); +jalview.schemes.ResidueProperties.Arg.add("CGC");jalview.schemes.ResidueProperties.Arg.add("CGT");jalview.schemes.ResidueProperties.Gly.add("GGA");jalview.schemes.ResidueProperties.Gly.add("GGG");jalview.schemes.ResidueProperties.Gly.add("GGC");jalview.schemes.ResidueProperties.Gly.add("GGT");jalview.schemes.ResidueProperties.STOP.add("TGA");jalview.schemes.ResidueProperties.STOP.add("TAA");jalview.schemes.ResidueProperties.STOP.add("TAG");jalview.schemes.ResidueProperties.Trp.add("TGG");jalview.schemes.ResidueProperties.Cys.add("TGC"); +jalview.schemes.ResidueProperties.Cys.add("TGT");jalview.schemes.ResidueProperties.Ile.add("ATA");jalview.schemes.ResidueProperties.Ile.add("ATC");jalview.schemes.ResidueProperties.Ile.add("ATT");jalview.schemes.ResidueProperties.Met.add("ATG");jalview.schemes.ResidueProperties.Leu.add("CTA");jalview.schemes.ResidueProperties.Leu.add("CTG");jalview.schemes.ResidueProperties.Leu.add("CTC");jalview.schemes.ResidueProperties.Leu.add("CTT");jalview.schemes.ResidueProperties.Leu.add("TTA");jalview.schemes.ResidueProperties.Leu.add("TTG"); +jalview.schemes.ResidueProperties.Val.add("GTA");jalview.schemes.ResidueProperties.Val.add("GTG");jalview.schemes.ResidueProperties.Val.add("GTC");jalview.schemes.ResidueProperties.Val.add("GTT");jalview.schemes.ResidueProperties.Phe.add("TTC");jalview.schemes.ResidueProperties.Phe.add("TTT");c$.propHash=c$.prototype.propHash=new java.util.Hashtable;c$.hydrophobic=c$.prototype.hydrophobic=new java.util.Hashtable;c$.polar=c$.prototype.polar=new java.util.Hashtable;c$.small=c$.prototype.small=new java.util.Hashtable; +c$.positive=c$.prototype.positive=new java.util.Hashtable;c$.negative=c$.prototype.negative=new java.util.Hashtable;c$.charged=c$.prototype.charged=new java.util.Hashtable;c$.aromatic=c$.prototype.aromatic=new java.util.Hashtable;c$.aliphatic=c$.prototype.aliphatic=new java.util.Hashtable;c$.tiny=c$.prototype.tiny=new java.util.Hashtable;c$.proline=c$.prototype.proline=new java.util.Hashtable;jalview.schemes.ResidueProperties.hydrophobic.put("I",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("L", +new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("V",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("C",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("A",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("G",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("M",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("F",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("Y",new Integer(1)); +jalview.schemes.ResidueProperties.hydrophobic.put("W",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("H",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("K",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("X",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("-",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("*",new Integer(1));jalview.schemes.ResidueProperties.hydrophobic.put("R",new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("E", +new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("Q",new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("D",new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("N",new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("S",new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("T",new Integer(0));jalview.schemes.ResidueProperties.hydrophobic.put("P",new Integer(0));jalview.schemes.ResidueProperties.polar.put("Y",new Integer(1));jalview.schemes.ResidueProperties.polar.put("W", +new Integer(1));jalview.schemes.ResidueProperties.polar.put("H",new Integer(1));jalview.schemes.ResidueProperties.polar.put("K",new Integer(1));jalview.schemes.ResidueProperties.polar.put("R",new Integer(1));jalview.schemes.ResidueProperties.polar.put("E",new Integer(1));jalview.schemes.ResidueProperties.polar.put("Q",new Integer(1));jalview.schemes.ResidueProperties.polar.put("D",new Integer(1));jalview.schemes.ResidueProperties.polar.put("N",new Integer(1));jalview.schemes.ResidueProperties.polar.put("S", +new Integer(1));jalview.schemes.ResidueProperties.polar.put("T",new Integer(1));jalview.schemes.ResidueProperties.polar.put("X",new Integer(1));jalview.schemes.ResidueProperties.polar.put("-",new Integer(1));jalview.schemes.ResidueProperties.polar.put("*",new Integer(1));jalview.schemes.ResidueProperties.polar.put("I",new Integer(0));jalview.schemes.ResidueProperties.polar.put("L",new Integer(0));jalview.schemes.ResidueProperties.polar.put("V",new Integer(0));jalview.schemes.ResidueProperties.polar.put("C", +new Integer(0));jalview.schemes.ResidueProperties.polar.put("A",new Integer(0));jalview.schemes.ResidueProperties.polar.put("G",new Integer(0));jalview.schemes.ResidueProperties.polar.put("M",new Integer(0));jalview.schemes.ResidueProperties.polar.put("F",new Integer(0));jalview.schemes.ResidueProperties.polar.put("P",new Integer(0));jalview.schemes.ResidueProperties.small.put("I",new Integer(0));jalview.schemes.ResidueProperties.small.put("L",new Integer(0));jalview.schemes.ResidueProperties.small.put("V", +new Integer(1));jalview.schemes.ResidueProperties.small.put("C",new Integer(1));jalview.schemes.ResidueProperties.small.put("A",new Integer(1));jalview.schemes.ResidueProperties.small.put("G",new Integer(1));jalview.schemes.ResidueProperties.small.put("M",new Integer(0));jalview.schemes.ResidueProperties.small.put("F",new Integer(0));jalview.schemes.ResidueProperties.small.put("Y",new Integer(0));jalview.schemes.ResidueProperties.small.put("W",new Integer(0));jalview.schemes.ResidueProperties.small.put("H", +new Integer(0));jalview.schemes.ResidueProperties.small.put("K",new Integer(0));jalview.schemes.ResidueProperties.small.put("R",new Integer(0));jalview.schemes.ResidueProperties.small.put("E",new Integer(0));jalview.schemes.ResidueProperties.small.put("Q",new Integer(0));jalview.schemes.ResidueProperties.small.put("D",new Integer(1));jalview.schemes.ResidueProperties.small.put("N",new Integer(1));jalview.schemes.ResidueProperties.small.put("S",new Integer(1));jalview.schemes.ResidueProperties.small.put("T", +new Integer(1));jalview.schemes.ResidueProperties.small.put("P",new Integer(1));jalview.schemes.ResidueProperties.small.put("-",new Integer(1));jalview.schemes.ResidueProperties.small.put("*",new Integer(1));jalview.schemes.ResidueProperties.positive.put("I",new Integer(0));jalview.schemes.ResidueProperties.positive.put("L",new Integer(0));jalview.schemes.ResidueProperties.positive.put("V",new Integer(0));jalview.schemes.ResidueProperties.positive.put("C",new Integer(0));jalview.schemes.ResidueProperties.positive.put("A", +new Integer(0));jalview.schemes.ResidueProperties.positive.put("G",new Integer(0));jalview.schemes.ResidueProperties.positive.put("M",new Integer(0));jalview.schemes.ResidueProperties.positive.put("F",new Integer(0));jalview.schemes.ResidueProperties.positive.put("Y",new Integer(0));jalview.schemes.ResidueProperties.positive.put("W",new Integer(0));jalview.schemes.ResidueProperties.positive.put("H",new Integer(1));jalview.schemes.ResidueProperties.positive.put("K",new Integer(1));jalview.schemes.ResidueProperties.positive.put("R", +new Integer(1));jalview.schemes.ResidueProperties.positive.put("E",new Integer(0));jalview.schemes.ResidueProperties.positive.put("Q",new Integer(0));jalview.schemes.ResidueProperties.positive.put("D",new Integer(0));jalview.schemes.ResidueProperties.positive.put("N",new Integer(0));jalview.schemes.ResidueProperties.positive.put("S",new Integer(0));jalview.schemes.ResidueProperties.positive.put("T",new Integer(0));jalview.schemes.ResidueProperties.positive.put("P",new Integer(0));jalview.schemes.ResidueProperties.positive.put("-", +new Integer(1));jalview.schemes.ResidueProperties.positive.put("*",new Integer(1));jalview.schemes.ResidueProperties.negative.put("I",new Integer(0));jalview.schemes.ResidueProperties.negative.put("L",new Integer(0));jalview.schemes.ResidueProperties.negative.put("V",new Integer(0));jalview.schemes.ResidueProperties.negative.put("C",new Integer(0));jalview.schemes.ResidueProperties.negative.put("A",new Integer(0));jalview.schemes.ResidueProperties.negative.put("G",new Integer(0));jalview.schemes.ResidueProperties.negative.put("M", +new Integer(0));jalview.schemes.ResidueProperties.negative.put("F",new Integer(0));jalview.schemes.ResidueProperties.negative.put("Y",new Integer(0));jalview.schemes.ResidueProperties.negative.put("W",new Integer(0));jalview.schemes.ResidueProperties.negative.put("H",new Integer(0));jalview.schemes.ResidueProperties.negative.put("K",new Integer(0));jalview.schemes.ResidueProperties.negative.put("R",new Integer(0));jalview.schemes.ResidueProperties.negative.put("E",new Integer(1));jalview.schemes.ResidueProperties.negative.put("Q", +new Integer(0));jalview.schemes.ResidueProperties.negative.put("D",new Integer(1));jalview.schemes.ResidueProperties.negative.put("N",new Integer(0));jalview.schemes.ResidueProperties.negative.put("S",new Integer(0));jalview.schemes.ResidueProperties.negative.put("T",new Integer(0));jalview.schemes.ResidueProperties.negative.put("P",new Integer(0));jalview.schemes.ResidueProperties.negative.put("-",new Integer(1));jalview.schemes.ResidueProperties.negative.put("*",new Integer(1));jalview.schemes.ResidueProperties.charged.put("I", +new Integer(0));jalview.schemes.ResidueProperties.charged.put("L",new Integer(0));jalview.schemes.ResidueProperties.charged.put("V",new Integer(0));jalview.schemes.ResidueProperties.charged.put("C",new Integer(0));jalview.schemes.ResidueProperties.charged.put("A",new Integer(0));jalview.schemes.ResidueProperties.charged.put("G",new Integer(0));jalview.schemes.ResidueProperties.charged.put("M",new Integer(0));jalview.schemes.ResidueProperties.charged.put("F",new Integer(0));jalview.schemes.ResidueProperties.charged.put("Y", +new Integer(0));jalview.schemes.ResidueProperties.charged.put("W",new Integer(0));jalview.schemes.ResidueProperties.charged.put("H",new Integer(1));jalview.schemes.ResidueProperties.charged.put("K",new Integer(1));jalview.schemes.ResidueProperties.charged.put("R",new Integer(1));jalview.schemes.ResidueProperties.charged.put("E",new Integer(1));jalview.schemes.ResidueProperties.charged.put("Q",new Integer(0));jalview.schemes.ResidueProperties.charged.put("D",new Integer(1));jalview.schemes.ResidueProperties.charged.put("N", +new Integer(0));jalview.schemes.ResidueProperties.charged.put("S",new Integer(0));jalview.schemes.ResidueProperties.charged.put("T",new Integer(0));jalview.schemes.ResidueProperties.charged.put("P",new Integer(0));jalview.schemes.ResidueProperties.charged.put("-",new Integer(1));jalview.schemes.ResidueProperties.charged.put("*",new Integer(1));jalview.schemes.ResidueProperties.aromatic.put("I",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("L",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("V", +new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("C",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("A",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("G",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("M",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("F",new Integer(1));jalview.schemes.ResidueProperties.aromatic.put("Y",new Integer(1));jalview.schemes.ResidueProperties.aromatic.put("W",new Integer(1));jalview.schemes.ResidueProperties.aromatic.put("H", +new Integer(1));jalview.schemes.ResidueProperties.aromatic.put("K",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("R",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("E",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("Q",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("D",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("N",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("S",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("T", +new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("P",new Integer(0));jalview.schemes.ResidueProperties.aromatic.put("-",new Integer(1));jalview.schemes.ResidueProperties.aromatic.put("*",new Integer(1));jalview.schemes.ResidueProperties.aliphatic.put("I",new Integer(1));jalview.schemes.ResidueProperties.aliphatic.put("L",new Integer(1));jalview.schemes.ResidueProperties.aliphatic.put("V",new Integer(1));jalview.schemes.ResidueProperties.aliphatic.put("C",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("A", +new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("G",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("M",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("F",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("Y",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("W",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("H",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("K",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("R", +new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("E",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("Q",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("D",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("N",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("S",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("T",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("P",new Integer(0));jalview.schemes.ResidueProperties.aliphatic.put("-", +new Integer(1));jalview.schemes.ResidueProperties.aliphatic.put("*",new Integer(1));jalview.schemes.ResidueProperties.tiny.put("I",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("L",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("V",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("C",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("A",new Integer(1));jalview.schemes.ResidueProperties.tiny.put("G",new Integer(1));jalview.schemes.ResidueProperties.tiny.put("M", +new Integer(0));jalview.schemes.ResidueProperties.tiny.put("F",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("Y",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("W",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("H",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("K",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("R",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("E",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("Q", +new Integer(0));jalview.schemes.ResidueProperties.tiny.put("D",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("N",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("S",new Integer(1));jalview.schemes.ResidueProperties.tiny.put("T",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("P",new Integer(0));jalview.schemes.ResidueProperties.tiny.put("-",new Integer(1));jalview.schemes.ResidueProperties.tiny.put("*",new Integer(1));jalview.schemes.ResidueProperties.proline.put("I", +new Integer(0));jalview.schemes.ResidueProperties.proline.put("L",new Integer(0));jalview.schemes.ResidueProperties.proline.put("V",new Integer(0));jalview.schemes.ResidueProperties.proline.put("C",new Integer(0));jalview.schemes.ResidueProperties.proline.put("A",new Integer(0));jalview.schemes.ResidueProperties.proline.put("G",new Integer(0));jalview.schemes.ResidueProperties.proline.put("M",new Integer(0));jalview.schemes.ResidueProperties.proline.put("F",new Integer(0));jalview.schemes.ResidueProperties.proline.put("Y", +new Integer(0));jalview.schemes.ResidueProperties.proline.put("W",new Integer(0));jalview.schemes.ResidueProperties.proline.put("H",new Integer(0));jalview.schemes.ResidueProperties.proline.put("K",new Integer(0));jalview.schemes.ResidueProperties.proline.put("R",new Integer(0));jalview.schemes.ResidueProperties.proline.put("E",new Integer(0));jalview.schemes.ResidueProperties.proline.put("Q",new Integer(0));jalview.schemes.ResidueProperties.proline.put("D",new Integer(0));jalview.schemes.ResidueProperties.proline.put("N", +new Integer(0));jalview.schemes.ResidueProperties.proline.put("S",new Integer(0));jalview.schemes.ResidueProperties.proline.put("T",new Integer(0));jalview.schemes.ResidueProperties.proline.put("P",new Integer(1));jalview.schemes.ResidueProperties.proline.put("-",new Integer(1));jalview.schemes.ResidueProperties.proline.put("*",new Integer(1));jalview.schemes.ResidueProperties.propHash.put("hydrophobic",jalview.schemes.ResidueProperties.hydrophobic);jalview.schemes.ResidueProperties.propHash.put("small", +jalview.schemes.ResidueProperties.small);jalview.schemes.ResidueProperties.propHash.put("positive",jalview.schemes.ResidueProperties.positive);jalview.schemes.ResidueProperties.propHash.put("negative",jalview.schemes.ResidueProperties.negative);jalview.schemes.ResidueProperties.propHash.put("charged",jalview.schemes.ResidueProperties.charged);jalview.schemes.ResidueProperties.propHash.put("aromatic",jalview.schemes.ResidueProperties.aromatic);jalview.schemes.ResidueProperties.propHash.put("aliphatic", +jalview.schemes.ResidueProperties.aliphatic);jalview.schemes.ResidueProperties.propHash.put("tiny",jalview.schemes.ResidueProperties.tiny);jalview.schemes.ResidueProperties.propHash.put("proline",jalview.schemes.ResidueProperties.proline);jalview.schemes.ResidueProperties.propHash.put("polar",jalview.schemes.ResidueProperties.polar);for(var b=w(23,23,0),c=w(23,23,0),f=w(23,23,0),a=0;23>a;a++){for(var l=0,k=0,g=0,e="",e=jalview.schemes.ResidueProperties.aa.length>a?e+jalview.schemes.ResidueProperties.aa[a]: +"-",j=a+1;23>j;j++){var n="",n=jalview.schemes.ResidueProperties.aa.length>j?n+jalview.schemes.ResidueProperties.aa[j]:"-";b[a][j]=0;c[a][j]=0;f[a][j]=0;for(var x=jalview.schemes.ResidueProperties.propHash.keys();x.hasMoreElements();){var u=x.nextElement(),D=jalview.schemes.ResidueProperties.propHash.get(u);null!=D.get(e)&&null!=D.get(n)&&(u=D.get(e).intValue(),D=D.get(n).intValue(),c[a][j]+=u==D&&0",">");jalview.schemes.ResidueProperties.toRNAssState.put("<",">"); +jalview.schemes.ResidueProperties.toRNAssState.put("A","A");jalview.schemes.ResidueProperties.toRNAssState.put("a","A");jalview.schemes.ResidueProperties.toRNAssState.put("B","B");jalview.schemes.ResidueProperties.toRNAssState.put("b","B");jalview.schemes.ResidueProperties.toRNAssState.put("C","C");jalview.schemes.ResidueProperties.toRNAssState.put("c","C");jalview.schemes.ResidueProperties.toRNAssState.put("D","D");jalview.schemes.ResidueProperties.toRNAssState.put("d","D");jalview.schemes.ResidueProperties.toRNAssState.put("E", +"E");jalview.schemes.ResidueProperties.toRNAssState.put("e","E");jalview.schemes.ResidueProperties.toRNAssState.put("F","F");jalview.schemes.ResidueProperties.toRNAssState.put("f","F");jalview.schemes.ResidueProperties.toRNAssState.put("G","G");jalview.schemes.ResidueProperties.toRNAssState.put("g","G");jalview.schemes.ResidueProperties.toRNAssState.put("H","H");jalview.schemes.ResidueProperties.toRNAssState.put("h","H");jalview.schemes.ResidueProperties.toRNAssState.put("I","I");jalview.schemes.ResidueProperties.toRNAssState.put("i", +"I");jalview.schemes.ResidueProperties.toRNAssState.put("J","J");jalview.schemes.ResidueProperties.toRNAssState.put("j","J");jalview.schemes.ResidueProperties.toRNAssState.put("K","K");jalview.schemes.ResidueProperties.toRNAssState.put("k","K");jalview.schemes.ResidueProperties.toRNAssState.put("L","L");jalview.schemes.ResidueProperties.toRNAssState.put("l","L");jalview.schemes.ResidueProperties.toRNAssState.put("M","M");jalview.schemes.ResidueProperties.toRNAssState.put("m","M");jalview.schemes.ResidueProperties.toRNAssState.put("N", +"N");jalview.schemes.ResidueProperties.toRNAssState.put("n","N");jalview.schemes.ResidueProperties.toRNAssState.put("O","O");jalview.schemes.ResidueProperties.toRNAssState.put("o","O");jalview.schemes.ResidueProperties.toRNAssState.put("P","P");jalview.schemes.ResidueProperties.toRNAssState.put("p","P");jalview.schemes.ResidueProperties.toRNAssState.put("Q","Q");jalview.schemes.ResidueProperties.toRNAssState.put("q","Q");jalview.schemes.ResidueProperties.toRNAssState.put("R","R");jalview.schemes.ResidueProperties.toRNAssState.put("r", +"R");jalview.schemes.ResidueProperties.toRNAssState.put("S","S");jalview.schemes.ResidueProperties.toRNAssState.put("s","S");jalview.schemes.ResidueProperties.toRNAssState.put("T","T");jalview.schemes.ResidueProperties.toRNAssState.put("t","T");jalview.schemes.ResidueProperties.toRNAssState.put("U","U");jalview.schemes.ResidueProperties.toRNAssState.put("u","U");jalview.schemes.ResidueProperties.toRNAssState.put("V","V");jalview.schemes.ResidueProperties.toRNAssState.put("v","V");jalview.schemes.ResidueProperties.toRNAssState.put("W", +"W");jalview.schemes.ResidueProperties.toRNAssState.put("w","W");jalview.schemes.ResidueProperties.toRNAssState.put("X","X");jalview.schemes.ResidueProperties.toRNAssState.put("x","X");jalview.schemes.ResidueProperties.toRNAssState.put("Y","Y");jalview.schemes.ResidueProperties.toRNAssState.put("y","Y");jalview.schemes.ResidueProperties.toRNAssState.put("Z","Z");jalview.schemes.ResidueProperties.toRNAssState.put("z","Z");for(a=0;aD.size()?u=D:(u=x,x=D);for(var m,D=x.keySet().iterator();D.hasNext()&& +((m=D.next())||1);)null!=u.get(m)&&n++;a[b][j]+=x.size()+u.size()-2*n;a[j][b]+=a[b][j]}}}for(b=0;b');for(var d="A";"Z">=d;d=String.fromCharCode(d.charCodeAt(0)+1))if(0<=c[d.charCodeAt(0)]&&c[d.charCodeAt(0)]":"");for(var g="A";"Z">=g;g=String.fromCharCode(g.charCodeAt(0)+1))0<=c[g.charCodeAt(0)]&&c[g.charCodeAt(0)] ":"\t")+g+(a?" ": 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this.sequence.length});d(c$,"setSequence",function(a){this.sequence=a.toCharArray();this.checkValidRange()},"~S");d(c$,"getSequenceAsString",function(){return String.instantialize(this.sequence)});d(c$,"getSequenceAsString",function(a,b){return String.instantialize(this.getSequence(a,b))},"~N,~N");d(c$,"getSequence",function(){return this.sequence});d(c$,"getSequence",function(a, +b){0>a&&(a=0);if(a>=this.sequence.length)return N(0,"\x00");b>=this.sequence.length&&(b=this.sequence.length);var c=N(b-a,"\x00");System.arraycopy(this.sequence,a,c,0,b-a);return c},"~N,~N");e(c$,"getSubSequence",function(a,b){0>a&&(a=0);var c=this.getSequence(a,b);if(0==c.length)return null;var f=this.findPosition(a),l=this.findPosition(b)-1,c=new jalview.datamodel.Sequence(this.getName(),c,f,l);c.setDescription(this.description);null!=this.datasetSequence?c.setDatasetSequence(this.datasetSequence): +c.setDatasetSequence(this);return c},"~N,~N");e(c$,"getCharAt",function(a){return 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+"_"==a?c:-1},"com.stevesoft.pat.StringLike,~N,~N");c$=B(com.stevesoft.pat,"NUnicodeW",com.stevesoft.pat.UniValidator);e(c$,"validate",function(a,b,c){if(b>=a.length())return-1;a=a.charAt(b);return!com.stevesoft.pat.Prop.isAlphabetic(a)&&!(com.stevesoft.pat.Prop.isDecimalDigit(a)||"_"==a)?c:-1},"com.stevesoft.pat.StringLike,~N,~N");c$=B(com.stevesoft.pat,"UnicodeDigit",com.stevesoft.pat.UniValidator);e(c$,"validate",function(a,b,c){return bthis.pt.lastPos&&(this.pt.lastPos=0);if((null==a?null:a.unwrap())!==(null==this.src?null:a.unwrap()))this.pt.lastPos=0;this.src=a;this.pt.dotDoesntMatchCR=com.stevesoft.pat.Regex.dotDoesntMatchCR&&!this.sFlag;this.pt.mFlag=(new Boolean(this.mFlag| +com.stevesoft.pat.Regex.defaultMFlag)).valueOf();this.pt.ignoreCase=this.ignoreCase;this.pt.no_check=!1;if(null!=this.pt.marks)for(var b=0;b=b&&(l=b);if(null==this.skipper)for(;b<=l;b++){if(this.charsMatched_=this.thePattern.matchAt(a,b,f),0<=this.charsMatched_)return this.matchFrom_=this.thePattern.mfrom,this.marks=f.marks,this.gFlagto=this.matchFrom_+this.charsMatched_,this.gFlags=a,this.didMatch_=!0}else for(f.no_check=!0;b<=l;b++){b=this.skipper.find(this.src,b,l);if(0>b){this.charsMatched_=this.matchFrom_=-1;break}this.charsMatched_=this.thePattern.matchAt(a,b,f);if(0<= +this.charsMatched_)return this.matchFrom_=this.thePattern.mfrom,this.marks=f.marks,this.gFlagto=this.matchFrom_+this.charsMatched_,this.gFlags=a,this.didMatch_=!0}return this.didMatch_=!1},"com.stevesoft.pat.StringLike,~N,~N");d(c$,"_reverseSearch",function(a,b,c){return this._reverseSearchLike(new com.stevesoft.pat.wrap.StringWrap(a),b,c)},"~S,~N,~N");d(c$,"_reverseSearchLike",function(a,b,c){this.gFlag&&(0=b;c--)if(this.charsMatched_=this.thePattern.matchAt(a,c,f),0<=this.charsMatched_)return this.matchFrom_=this.thePattern.mfrom,this.marks=f.marks,this.gFlagto=this.matchFrom_-1,this.gFlags=a,this.didMatch_=!0;return this.didMatch_=!1},"com.stevesoft.pat.StringLike,~N,~N");c$.setCbits=d(c$,"setCbits",function(a,b){if(a===com.stevesoft.pat.Regex.lasts)b.cbits=com.stevesoft.pat.Regex.lastbs;else{for(var c=new java.util.BitSet(a.length()),f=" ",l=!1,d=0;d"))c=a.getPatInt(),null==c&&com.stevesoft.pat.RegSyntaxError.endItAll("No int after (?>"),this.add(new com.stevesoft.pat.Backup(-c.intValue())), +a.match(")")||com.stevesoft.pat.RegSyntaxError.endItAll("No ) after (?<");else if(a.incMatch("(?@")){c=a.c;a.inc();var f=a.c;a.inc();a.match(")")||com.stevesoft.pat.RegSyntaxError.endItAll("(?@ does not have closing paren");this.add(new com.stevesoft.pat.Group(c,f))}else if(a.incMatch("(?#"))for(;!a.match(")");)a.inc();else if(a.dontMatch&&"w"==a.c)c=new com.stevesoft.pat.Bracket(!1),c.addOr(new com.stevesoft.pat.Range("a","z")),c.addOr(new com.stevesoft.pat.Range("A","Z")),c.addOr(new com.stevesoft.pat.Range("0", +"9")),c.addOr(new com.stevesoft.pat.oneChar("_")),this.add(c);else if(a.dontMatch&&"G"==a.c)this.add(new com.stevesoft.pat.BackG);else if(a.dontMatch&&"s"==a.c)c=new com.stevesoft.pat.Bracket(!1),c.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(32))),c.addOr(new com.stevesoft.pat.Range(String.fromCharCode(8),String.fromCharCode(10))),c.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(13))),this.add(c);else if(a.dontMatch&&"d"==a.c)c=new com.stevesoft.pat.Range("0","9"),c.printBrackets= +!0,this.add(c);else if(a.dontMatch&&"W"==a.c)c=new com.stevesoft.pat.Bracket(!0),c.addOr(new com.stevesoft.pat.Range("a","z")),c.addOr(new com.stevesoft.pat.Range("A","Z")),c.addOr(new com.stevesoft.pat.Range("0","9")),c.addOr(new com.stevesoft.pat.oneChar("_")),this.add(c);else if(a.dontMatch&&"S"==a.c)c=new com.stevesoft.pat.Bracket(!0),c.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(32))),c.addOr(new com.stevesoft.pat.Range(String.fromCharCode(8),String.fromCharCode(10))),c.addOr(new com.stevesoft.pat.oneChar(String.fromCharCode(13))), 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com.stevesoft.pat.End(!1));else if(a.match("."))this.add(new com.stevesoft.pat.Any); +else if(a.incMatch("(??")){c=new StringBuffer;for(f=new StringBuffer;!a.match(")")&&!a.match(":");)c.append(a.c),a.inc();if(a.incMatch(":"))for(;!a.match(")");)f.append(a.c),a.inc();var l=c.toString();v(com.stevesoft.pat.Regex.validators.get(l),String)?(c=com.stevesoft.pat.Regex.validators.get(l),f=new com.stevesoft.pat.Regex(null,""),l=new com.stevesoft.pat.Rthings(this),l.noBackRefs=!0,f._compile(c,l),this.add(f.thePattern)):(c=new com.stevesoft.pat.Custom(c.toString()),null!=c.v&&(l=c.v.arg(f.toString()), +null!=l&&(l.argsave=f.toString(),f=c.v.pattern,c.v=l,l.pattern=f),f=new com.stevesoft.pat.Regex(null,""),l=new com.stevesoft.pat.Rthings(this),l.noBackRefs=!0,f._compile(c.v.pattern,l),c.sub=f.thePattern,c.sub.add(new com.stevesoft.pat.CustomEndpoint(c)),c.sub.setParent(c),this.add(c)))}else if(a.match("(")){b.parenLevel++;f=new com.stevesoft.pat.Regex(null,"");a.inc();if(a.incMatch("?:"))f.or=new com.stevesoft.pat.Or;else if(a.incMatch("?="))f.or=new com.stevesoft.pat.lookAhead(!1);else if(a.incMatch("?!"))f.or= +new com.stevesoft.pat.lookAhead(!0);else if(a.match("?")){a.inc();do"i"==a.c&&(b.ignoreCase=!0),"Q"==a.c&&(b.dontMatchInQuotes=!0),"o"==a.c&&(b.optimizeMe=!0),"g"==a.c&&(b.gFlag=!0),"s"==a.c&&(b.sFlag=!0),"m"==a.c&&(b.mFlag=!0),a.inc();while(!a.match(")")&&!a.$eos);f=null;b.parenLevel--;a.$eos&&com.stevesoft.pat.RegSyntaxError.endItAll("Unclosed ()")}else f.or=b.noBackRefs?new com.stevesoft.pat.Or:new com.stevesoft.pat.OrMark(b.val++);null!=f&&this.add(f._compileSP(a,b))}else if(a.match("^"))this.add(new com.stevesoft.pat.Start(!0)); +else if(a.dontMatch&&"A"==a.c)this.add(new com.stevesoft.pat.Start(!1));else if(a.match("*"))this.addMulti(new com.stevesoft.pat.patInt(0),new com.stevesoft.pat.patInf);else if(a.match("+"))this.addMulti(new com.stevesoft.pat.patInt(1),new com.stevesoft.pat.patInf);else if(a.match("?"))this.addMulti(new com.stevesoft.pat.patInt(0),new com.stevesoft.pat.patInt(1));else if(a.match("{")){f=!1;c=new com.stevesoft.pat.StrPos(a);a.inc();var l=a.getPatInt(),d=null;a.match("}")?d=l:(a.match(",")||(f=!0), +a.inc(),d=a.match("}")?new com.stevesoft.pat.patInf:a.getPatInt());if(null==l||null==d)f=!0;f?(a.dup(c),this.add(new com.stevesoft.pat.oneChar(a.c))):this.addMulti(l,d)}else a.escMatch("x")&&this.next2Hex(a)?(a.inc(),f=this.getHexDigit(a),a.inc(),f=16*f+this.getHexDigit(a),this.add(new com.stevesoft.pat.oneChar(String.fromCharCode(f)))):a.escMatch("c")?(a.inc(),a.c.charCodeAt(0)=a.c||"a"<=a.c&&"f">=a.c||"A"<=a.c&&"F">=a.c)},"com.stevesoft.pat.StrPos");d(c$,"isOctalDigit",function(a,b){return!a.$eos&&!(new Boolean(b^a.dontMatch)).valueOf()&&"0"<=a.c&&"7">=a.c},"com.stevesoft.pat.StrPos,~B");d(c$,"getHexDigit",function(a){return"0"<=a.c&& 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com.stevesoft.pat.UnicodeW); +com.stevesoft.pat.Regex.defineV("W","(?>1)",new com.stevesoft.pat.NUnicodeW);com.stevesoft.pat.Regex.defineV("d","(?>1)",new com.stevesoft.pat.UnicodeDigit);com.stevesoft.pat.Regex.defineV("D","(?>1)",new com.stevesoft.pat.NUnicodeDigit);com.stevesoft.pat.Regex.defineV("m","(?>1)",new com.stevesoft.pat.UnicodeMath);com.stevesoft.pat.Regex.defineV("M","(?>1)",new com.stevesoft.pat.NUnicodeMath);com.stevesoft.pat.Regex.defineV("c","(?>1)",new com.stevesoft.pat.UnicodeCurrency);com.stevesoft.pat.Regex.defineV("C", +"(?>1)",new com.stevesoft.pat.NUnicodeCurrency);com.stevesoft.pat.Regex.defineV("a","(?>1)",new com.stevesoft.pat.UnicodeAlpha);com.stevesoft.pat.Regex.defineV("A","(?>1)",new com.stevesoft.pat.NUnicodeAlpha);com.stevesoft.pat.Regex.defineV("uc","(?>1)",new com.stevesoft.pat.UnicodeUpper);com.stevesoft.pat.Regex.defineV("lc","(?>1)",new com.stevesoft.pat.UnicodeLower);G(c$,"defaultMFlag",!1,"dotDoesntMatchCR",!0,"lasts",null,"lastbs",null,"back_slash","\\")});p("com.stevesoft.pat");q(null,"com.stevesoft.pat.RegRes", +["java.lang.StringBuffer"],function(){c$=s(function(){this.marks=null;this.didMatch_=!1;this.src=null;this.numSubs_=this.matchFrom_=this.charsMatched_=0;r(this,arguments)},com.stevesoft.pat,"RegRes");d(c$,"getString",function(){return this.src.toString()});d(c$,"getStringLike",function(){return this.src});e(c$,"toString",function(){var a=new StringBuffer;a.append("match="+this.matchedFrom()+":"+this.charsMatched());if(!this.didMatch())return a.toString();for(var b=0;ba||0>b?null:this.src.substring(a,a+b)});d(c$, +"matchedFromI",function(a){return null==this.marks||a>this.numSubs_?-1:this.marks[a]},"~N");d(c$,"charsMatchedI",function(a){return 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com.stevesoft.pat.patInt(1)})});p("com.stevesoft.pat");q(null,"com.stevesoft.pat.Validator", +["com.stevesoft.pat.patInf","$.patInt"],function(){c$=s(function(){this.argsave=null;this.pattern=".";r(this,arguments)},com.stevesoft.pat,"Validator");d(c$,"validate",function(a,b,c){return c},"com.stevesoft.pat.StringLike,~N,~N");d(c$,"arg",function(){return null},"~S");d(c$,"minChars",function(){return new com.stevesoft.pat.patInt(0)});d(c$,"maxChars",function(){return new com.stevesoft.pat.patInf})});p("com.stevesoft.pat");q(["com.stevesoft.pat.patInt"],"com.stevesoft.pat.patInf",null,function(){c$= +B(com.stevesoft.pat,"patInf",com.stevesoft.pat.patInt);m(c$,function(){t(this,com.stevesoft.pat.patInf,[]);this.inf=!0})});p("com.stevesoft.pat");c$=s(function(){this.i=0;this.inf=!1;r(this,arguments)},com.stevesoft.pat,"patInt");m(c$,function(){this.i=0;this.inf=!1});m(c$,function(a){this.i=a;this.inf=!1},"~N");m(c$,function(a){this.i=a.i;this.inf=a.inf},"com.stevesoft.pat.patInt");d(c$,"setInf",function(a){if(this.inf=a)this.i=2147483647},"~B");d(c$,"inc",function(){this.inf||this.i++});d(c$,"dec", +function(){this.inf||this.i--});d(c$,"lessEq",function(a){return!this.inf&&(a.inf||this.i<=a.i)},"com.stevesoft.pat.patInt");d(c$,"equals",function(a){return!a.inf&&!this.inf&&this.i==a.i},"com.stevesoft.pat.patInt");e(c$,"toString",function(){return this.inf?"":""+this.i});d(c$,"pluseq",function(a){this.inf||a.inf?this.setInf(!0):this.i+=a.i;return this},"com.stevesoft.pat.patInt");d(c$,"mul",function(a){return this.inf||a.inf?new com.stevesoft.pat.patInf:new com.stevesoft.pat.patInt(this.i*a.i)}, +"com.stevesoft.pat.patInt");d(c$,"mineq",function(a){if(a.inf)return this;this.inf?this.i=a.i:a.ithis.i&&(this.i=a.i);return this},"com.stevesoft.pat.patInt");d(c$,"finite",function(){return!this.inf});d(c$,"intValue",function(){return this.inf?2147483647:this.i});p("jalview.jsdev.api");M(jalview.jsdev.api,"RegExpInterface");p("com.stevesoft.pat"); +q(["com.stevesoft.pat.Pattern"],"com.stevesoft.pat.NoPattern",null,function(){c$=B(com.stevesoft.pat,"NoPattern",com.stevesoft.pat.Pattern);e(c$,"toString",function(){return"(?e=#)[^#d#D]"});e(c$,"matchInternal",function(){return-1},"~N,com.stevesoft.pat.Pthings");e(c$,"clone1",function(){return new com.stevesoft.pat.NoPattern},"java.util.Hashtable")});p("com.stevesoft.pat");q(null,"com.stevesoft.pat.Pattern",["com.stevesoft.pat.MessageManager","$.patInf","$.patInt","java.lang.Error","$.StringBuffer"], +function(){c$=s(function(){this.parent=this.next=null;this.mfrom=0;r(this,arguments)},com.stevesoft.pat,"Pattern");d(c$,"getNext",function(){return null!=this.next?this.next:null==this.parent?null:this.parent.getNext()});d(c$,"setParent",function(a){null!=this.next?this.next.setParent(a):this.parent=a},"com.stevesoft.pat.Pattern");d(c$,"nextMatch",function(a,b){var c=this.getNext();return null==c?a:c.matchInternal(a,b)},"~N,com.stevesoft.pat.Pthings");d(c$,"nextString",function(){return null==this.next? +"":this.next.toString()});c$.inString=d(c$,"inString",function(a,b){var c;for(c=0;ca)return-1;this.mfrom=aa&&(c.marks= +f);return a},"com.stevesoft.pat.Pattern,~N,com.stevesoft.pat.Pthings");d(c$,"clone1",function(){throw Error(com.stevesoft.pat.MessageManager.formatMessage("error.no_such_method_as_clone1_for",E(-1,[this.getClass().getName()])));},"java.util.Hashtable");d(c$,"clone",function(a){var b=a.get(this);if(null!=b)return b;b=this.clone1(a);if(null==b)throw Error(com.stevesoft.pat.MessageManager.getString("error.null_from_clone1"));a.put(this,b);a.put(b,b);null!=this.next&&(b.next=this.next.clone(a));null!= +this.parent&&(b.parent=this.parent.clone(a));return b},"java.util.Hashtable");e(c$,"equals",function(a){return a===this},"~O");G(c$,"ESC","\\","PROTECT_THESE",'[]{}(),$,-"^.')});p("com.stevesoft.pat");c$=B(com.stevesoft.pat,"MessageManager");c$.getString=d(c$,"getString",function(a){return a},"~S");c$.formatMessage=d(c$,"formatMessage",function(a,b){for(var c=0;cc||0>f||a+f>b.src.length())return-1;var l=b.src.length()-a;fthis.bk?">"+-this.bk:"<"+this.bk)+")"+this.nextString()});e(c$,"matchInternal",function(a,b){return a=a||"A"<=a&&"Z">=a||"0"<=a&&"9">=a||"_"==a?!0:!1},"~S");d(c$,"matchLeft",function(a,b){return 0>=a?!0:this.isAChar(b.src.charAt(a))&&this.isAChar(b.src.charAt(a-1))?!1:!0},"~N,com.stevesoft.pat.Pthings");d(c$,"matchRight",function(a,b){return 0>a?!1:a+1>=b.src.length()?!0:this.isAChar(b.src.charAt(a))&& 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this.neg&&0>c||!this.neg&&0<=c?this.nextMatch(a+1,b):-1},"~N,com.stevesoft.pat.Pthings"); +e(c$,"minChars",function(){return new com.stevesoft.pat.patInt(1)});e(c$,"maxChars",function(){return new com.stevesoft.pat.patInt(1)});e(c$,"addOr",function(a){this.pv=null;this.v.addElement(a);a.setParent(null);return this},"com.stevesoft.pat.Pattern");e(c$,"clone1",function(a){var b=new com.stevesoft.pat.Bracket(this.neg);b.v=new java.util.Vector;for(var c=0;cf.length()||c+d>a.length())return!1;if(b)for(b=l;bf.length()||c+d>a.length)return!1;if(b)for(b=l;bf.length||c+d>a.length())return!1;if(b)for(b=l;b< +g;b++){if(com.stevesoft.pat.CaseMgr.toLowerCaseC(f.charAt(b))!=com.stevesoft.pat.CaseMgr.toLowerCaseC(a.charAt(c++)))return!1}else for(b=l;bf.length||c+d>a.length)return!1;if(b)for(b=l;bl;){f=this.submatchInternal(f,b);if(0>f)return-1;l++}if(0> +f)return-1;c=this.nextMatch(f,b);if(0<=c)return c;if(this.mostMatches.finite())for(;0f)break;l++;if(l>this.mostMatches.intValue())break;c=this.nextMatch(f,b);if(0<=c)return c}else for(;0<=f;){f=this.submatchInternal(f,b);if(0>f)break;c=this.nextMatch(f,b);if(0<=c)return c}return-1}for(l=0;this.fewestMatches.intValue()>l;)if(f=this.submatchInternal(f,b),0<=f)l++;else return-1;c=f;if(this.mostMatches.finite())for(;l=a;){f=this.nextMatch(c,b);if(0<=f)return f;c-=1;l--;if(ll;)if(f=this.sub.matchInternal(f,b),0<=f)l++;else return-1;c=f;if(this.mostMatches.finite())for(;l=a;){f=this.nextMatch(c,b);if(0<=f)return f;c-=this.step;l--;if(l"+b);b=new com.stevesoft.pat.patInt(-1);a.lessEq(b)&&com.stevesoft.pat.RegSyntaxError.endItAll("Bad Multi Args: "+a+"< 0")},"com.stevesoft.pat.patInt,com.stevesoft.pat.patInt,com.stevesoft.pat.Pattern");d(c$,"getNext",function(){return this.nextRet});e(c$,"matchInternal",function(a,b){this.sub.setParent(this); +var c=-1;if(0<=this.pos_old&&a==this.pos_old)return-1;this.pos_old=a;this.matchMin.lessEq(this.count)&&(c=a);if(!this.count.lessEq(this.matchMax)||a>b.src.length())return-1;if((this.matchFewest||this.count.equals(this.matchMax))&&0<=c){var f=K(this,com.stevesoft.pat.Multi_stage2,"getNext",[]);if(null==f)return c;c=this.testMatch(f,a,b);if(0<=c)return c;c=-1}this.count.inc();try{if(this.count.lessEq(this.matchMax)){var d=this.testMatch(this.sub,a,b);if(0<=d)return d}}finally{this.count.dec()}if(!this.matchFewest&& +0<=c){f=K(this,com.stevesoft.pat.Multi_stage2,"getNext",[]);if(null==f)return c;c=this.testMatch(f,a,b)}return c},"~N,com.stevesoft.pat.Pthings");e(c$,"clone1",function(a){try{var b=new com.stevesoft.pat.Multi_stage2(this.matchMin,this.matchMax,this.sub.clone(a));b.matchFewest=this.matchFewest;return b}catch(c){if(y(c,com.stevesoft.pat.RegSyntax))return null;throw c;}},"java.util.Hashtable")});p("com.stevesoft.pat");q(["com.stevesoft.pat.Pattern"],"com.stevesoft.pat.NullPattern",["com.stevesoft.pat.patInt"], +function(){c$=B(com.stevesoft.pat,"NullPattern",com.stevesoft.pat.Pattern);e(c$,"toString",function(){return this.nextString()});e(c$,"matchInternal",function(a,b){return this.nextMatch(a,b)},"~N,com.stevesoft.pat.Pthings");e(c$,"maxChars",function(){return new com.stevesoft.pat.patInt(0)});e(c$,"clone1",function(){return new com.stevesoft.pat.NullPattern},"java.util.Hashtable")});p("com.stevesoft.pat");q(["com.stevesoft.pat.Or","$.SubMark"],"com.stevesoft.pat.OrMark",null,function(){c$=s(function(){this.sm= +null;this.id=0;r(this,arguments)},com.stevesoft.pat,"OrMark",com.stevesoft.pat.Or);J(c$,function(){this.sm=new com.stevesoft.pat.SubMark});m(c$,function(a){t(this,com.stevesoft.pat.OrMark,[]);this.sm.om=this;this.id=a},"~N");e(c$,"leftForm",function(){return"("});d(c$,"getNext",function(){return 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com.stevesoft.pat.Bits.decimal_digit.get(a.charCodeAt(0))},"~S");c$.isAlphabetic=d(c$,"isAlphabetic",function(a){null==com.stevesoft.pat.Bits.letter&&com.stevesoft.pat.Bits.letter_f();return com.stevesoft.pat.Bits.letter.get(a.charCodeAt(0))},"~S");c$.isMath=d(c$,"isMath",function(a){null==com.stevesoft.pat.Bits.math&&com.stevesoft.pat.Bits.math_f(); +return com.stevesoft.pat.Bits.math.get(a.charCodeAt(0))},"~S");c$.isCurrency=d(c$,"isCurrency",function(a){null==com.stevesoft.pat.Bits.currency&&com.stevesoft.pat.Bits.currency_f();return com.stevesoft.pat.Bits.currency.get(a.charCodeAt(0))},"~S");c$.isWhite=d(c$,"isWhite",function(a){null==com.stevesoft.pat.Bits.white&&com.stevesoft.pat.Bits.white_f();return com.stevesoft.pat.Bits.white.get(a.charCodeAt(0))},"~S");c$.isPunct=d(c$,"isPunct",function(a){null==com.stevesoft.pat.Bits.punct&&com.stevesoft.pat.Bits.punct_f(); +return com.stevesoft.pat.Bits.punct.get(a.charCodeAt(0))},"~S")});p("com.stevesoft.pat");c$=s(function(){this.carray=null;r(this,arguments)},com.stevesoft.pat,"Bits");m(c$,function(a){this.carray=a},"~A");d(c$,"get",function(a){return 0!=(this.carray[a>>4].charCodeAt(0)&1<<(a&15))},"~N");d(c$,"set",function(a,b){this.carray[a>>4]=b?String.fromCharCode(this.carray[a>>4].charCodeAt(0)|String.fromCharCode(1).charCodeAt(0)<<(a&15)):String.fromCharCode(this.carray[a>>4].charCodeAt(0)&String.fromCharCode(~(1<< +(a&15))).charCodeAt(0))},"~N,~B");c$.upper_f=d(c$,"upper_f",function(){var a=N(4159,"\x00");com.stevesoft.pat.Bits.upper=new 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com.stevesoft.pat.Bits(a);a[6]=String.fromCharCode(65534);a[7]=String.fromCharCode(2047);a[10]=String.fromCharCode(1024);a[11]=String.fromCharCode(1056);a[13]=String.fromCharCode(32768);a[14]=String.fromCharCode(65535); +a[15]=String.fromCharCode(65407);a[16]=String.fromCharCode(43690);a[17]=String.fromCharCode(43690);a[18]=String.fromCharCode(43690);a[19]=String.fromCharCode(21930);a[20]=String.fromCharCode(43861);a[21]=String.fromCharCode(43690);a[22]=String.fromCharCode(43690);a[23]=String.fromCharCode(54442);a[24]=String.fromCharCode(12585);a[25]=String.fromCharCode(20004);a[26]=String.fromCharCode(10538);a[27]=String.fromCharCode(9809);a[28]=String.fromCharCode(21056);a[29]=String.fromCharCode(46421);a[30]=String.fromCharCode(43690); 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com.stevesoft.pat.Bits(a);a[6]=String.fromCharCode(65534);a[7]=String.fromCharCode(2047);a[10]=String.fromCharCode(1024);a[11]=String.fromCharCode(1056);a[13]=String.fromCharCode(32768);a[14]=String.fromCharCode(65535);a[15]=String.fromCharCode(65407);a[16]=String.fromCharCode(43690);a[17]=String.fromCharCode(43690); +a[18]=String.fromCharCode(43690);a[19]=String.fromCharCode(21930);a[20]=String.fromCharCode(43861);a[21]=String.fromCharCode(43690);a[22]=String.fromCharCode(43690);a[23]=String.fromCharCode(54442);a[24]=String.fromCharCode(12585);a[25]=String.fromCharCode(20004);a[26]=String.fromCharCode(10538);a[27]=String.fromCharCode(9809);a[28]=String.fromCharCode(21056);a[29]=String.fromCharCode(46421);a[30]=String.fromCharCode(43690);a[31]=String.fromCharCode(43049);a[32]=String.fromCharCode(43690);a[33]=String.fromCharCode(170); 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com.stevesoft.pat.Bits(a);a[2]=String.fromCharCode(16);a[10]=String.fromCharCode(60);a[159]=String.fromCharCode(12);a[227]=String.fromCharCode(32768);a[522]=String.fromCharCode(8191);a[4070]=String.fromCharCode(512);a[4080]=String.fromCharCode(16);a[4094]="c";a[4098]=String.fromCharCode(16);a[4106]=String.fromCharCode(60)});c$.decimal_digit_f=d(c$,"decimal_digit_f", +function(){var a=N(4159,"\x00");com.stevesoft.pat.Bits.decimal_digit=new com.stevesoft.pat.Bits(a);a[3]=String.fromCharCode(1023);a[102]=String.fromCharCode(1023);a[111]=String.fromCharCode(1023);a[150]=String.fromCharCode(65472);a[158]=String.fromCharCode(65472);a[166]=String.fromCharCode(65472);a[174]=String.fromCharCode(65472);a[182]=String.fromCharCode(65472);a[190]=String.fromCharCode(65408);a[198]=String.fromCharCode(65472);a[206]=String.fromCharCode(65472);a[214]=String.fromCharCode(65472); 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+a[4106]=String.fromCharCode(1024);a[4107]=String.fromCharCode(1056);a[4108]=String.fromCharCode(65535);a[4109]=String.fromCharCode(65407);a[4110]=String.fromCharCode(65535);a[4111]=String.fromCharCode(65407);a[4112]=String.fromCharCode(65535);a[4113]=String.fromCharCode(65535);a[4114]=String.fromCharCode(65535);a[4115]=String.fromCharCode(65535);a[4116]=String.fromCharCode(65535);a[4117]=String.fromCharCode(65535);a[4118]=String.fromCharCode(65535);a[4119]=String.fromCharCode(65535);a[4120]=String.fromCharCode(65535); +a[4121]=String.fromCharCode(65535);a[4122]=String.fromCharCode(65535);a[4123]=String.fromCharCode(65535);a[4124]=String.fromCharCode(65535);a[4125]=String.fromCharCode(65535);a[4126]=String.fromCharCode(65535);a[4127]=String.fromCharCode(64575);a[4128]=String.fromCharCode(65535);a[4129]=String.fromCharCode(255);a[4133]=String.fromCharCode(65535);a[4134]=String.fromCharCode(65535);a[4135]=String.fromCharCode(65535);a[4136]=String.fromCharCode(65535);a[4137]=String.fromCharCode(65535);a[4138]=String.fromCharCode(511); +a[4139]=String.fromCharCode(63999);a[4140]=String.fromCharCode(3);a[4141]=String.fromCharCode(3);a[4142]=String.fromCharCode(31);a[4151]=String.fromCharCode(1024);a[4152]=String.fromCharCode(55104);a[4153]=String.fromCharCode(65535);a[4154]=String.fromCharCode(65531);a[4155]=String.fromCharCode(65535);a[4156]=String.fromCharCode(32767);a[4157]=String.fromCharCode(21631);a[4158]=String.fromCharCode(253)});c$.white_f=d(c$,"white_f",function(){var a=N(4159,"\x00");com.stevesoft.pat.Bits.white=new com.stevesoft.pat.Bits(a); +a[0]=String.fromCharCode(15872);a[1]=String.fromCharCode(61440);a[2]=String.fromCharCode(1);a[512]=String.fromCharCode(4095);a[514]=String.fromCharCode(768);a[768]=String.fromCharCode(1);a[4096]=String.fromCharCode(15872);a[4097]=String.fromCharCode(61440);a[4098]=String.fromCharCode(1)});c$.punct_f=d(c$,"punct_f",function(){var a=N(4159,"\x00");com.stevesoft.pat.Bits.punct=new com.stevesoft.pat.Bits(a);a[2]=String.fromCharCode(63470);a[3]=String.fromCharCode(35840);a[4]=String.fromCharCode(1);a[5]= +String.fromCharCode(47104);a[7]=String.fromCharCode(10240);a[10]=String.fromCharCode(10242);a[11]=String.fromCharCode(34944);a[55]=String.fromCharCode(16432);a[56]=String.fromCharCode(128);a[85]=String.fromCharCode(64512);a[88]=String.fromCharCode(512);a[91]=String.fromCharCode(16384);a[92]=String.fromCharCode(9);a[95]=String.fromCharCode(24);a[96]=String.fromCharCode(4096);a[97]=String.fromCharCode(34816);a[102]=String.fromCharCode(15360);a[109]=String.fromCharCode(16);a[150]="0";a[151]=String.fromCharCode(1); +a[226]=String.fromCharCode(32768);a[229]=String.fromCharCode(3072);a[234]=String.fromCharCode(32768);a[240]=String.fromCharCode(65520);a[241]=String.fromCharCode(7);a[243]=String.fromCharCode(15360);a[248]=String.fromCharCode(32);a[271]=String.fromCharCode(2048);a[513]=String.fromCharCode(65535);a[514]=String.fromCharCode(255);a[515]=String.fromCharCode(65535);a[516]="o";a[519]=String.fromCharCode(24576);a[520]=String.fromCharCode(24576);a[562]=String.fromCharCode(1536);a[768]=String.fromCharCode(65358); +a[769]=String.fromCharCode(65523);a[771]=String.fromCharCode(1);a[783]=String.fromCharCode(2048);a[4051]=String.fromCharCode(49152);a[4067]=String.fromCharCode(65535);a[4068]=String.fromCharCode(65055);a[4069]=String.fromCharCode(65527);a[4070]=String.fromCharCode(3339);a[4080]=String.fromCharCode(63470);a[4081]=String.fromCharCode(35840);a[4082]=String.fromCharCode(1);a[4083]=String.fromCharCode(47104);a[4085]=String.fromCharCode(10240);a[4086]=String.fromCharCode(62);a[4098]=String.fromCharCode(63470); +a[4099]=String.fromCharCode(35840);a[4100]=String.fromCharCode(1);a[4101]=String.fromCharCode(47104);a[4103]=String.fromCharCode(10240);a[4106]=String.fromCharCode(10242);a[4107]=String.fromCharCode(34944);a[4151]=String.fromCharCode(16432);a[4152]=String.fromCharCode(128)});G(c$,"upper",null,"lower",null,"title",null,"currency",null,"decimal_digit",null,"math",null,"letter",null,"white",null,"punct",null);p("com.stevesoft.pat");q(["com.stevesoft.pat.Pattern","$.RegSyntax"],["com.stevesoft.pat.BadRangeArgs", +"$.Range"],["com.stevesoft.pat.RegSyntaxError","$.oneChar","$.patInt"],function(){c$=B(com.stevesoft.pat,"BadRangeArgs",com.stevesoft.pat.RegSyntax);c$=s(function(){this.althi=this.altlo=this.hi=this.lo="\x00";this.printBrackets=!1;r(this,arguments)},com.stevesoft.pat,"Range",com.stevesoft.pat.Pattern);e(c$,"toString",function(){var a=com.stevesoft.pat.Pattern.protect(""+this.lo,'[]{}(),$,-"^.',"\\")+"-"+com.stevesoft.pat.Pattern.protect(""+this.hi,'[]{}(),$,-"^.',"\\");return!this.printBrackets? +a:"["+a+"]"});m(c$,function(a,b){t(this,com.stevesoft.pat.Range,[]);this.lo=a;this.hi=b;var c=null;this.lo>=this.hi&&com.stevesoft.pat.RegSyntaxError.endItAll("Badly formed []'s : "+this.lo+" >= "+this.hi);c=new com.stevesoft.pat.oneChar(this.lo);this.altlo=c.altc;c=new com.stevesoft.pat.oneChar(this.hi);this.althi=c.altc},"~S,~S");e(c$,"matchInternal",function(a,b){if(a>=b.src.length()||this.Masked(a,b))return-1;var c=b.src.charAt(a);return this.lo<=c&&c<=this.hi||b.ignoreCase&&this.altlo<=c&&c<= +this.althi?this.nextMatch(a+1,b):-1},"~N,com.stevesoft.pat.Pthings");e(c$,"minChars",function(){return new com.stevesoft.pat.patInt(1)});e(c$,"maxChars",function(){return new com.stevesoft.pat.patInt(1)});e(c$,"clone1",function(){try{var a=new com.stevesoft.pat.Range(this.lo,this.hi);a.printBrackets=this.printBrackets;return a}catch(b){if(y(b,com.stevesoft.pat.RegSyntax))return null;throw b;}},"java.util.Hashtable")});p("com.stevesoft.pat");q(["com.stevesoft.pat.Pattern"],"com.stevesoft.pat.oneChar", +["com.stevesoft.pat.CaseMgr","$.patInt"],function(){c$=s(function(){this.altc2=this.altc=this.c="\x00";this.mask=0;r(this,arguments)},com.stevesoft.pat,"oneChar",com.stevesoft.pat.Pattern);m(c$,function(a){t(this,com.stevesoft.pat.oneChar,[]);this.c=a;var b,c;a=com.stevesoft.pat.CaseMgr.toUpperCaseC(this.c);b=com.stevesoft.pat.CaseMgr.toLowerCaseC(this.c);c=com.stevesoft.pat.CaseMgr.toTitleCaseC(this.c);this.c==a?(this.altc=b,this.altc2=c):this.c==b?(this.altc=a,this.altc2=c):(this.altc=b,this.altc2= +a);this.mask=this.c.charCodeAt(0)&this.altc.charCodeAt(0)&this.altc2.charCodeAt(0)},"~S");e(c$,"matchInternal",function(a,b){var c,f=-1;if(a=b.src.length())return-1;var c=this.h.get(new Character(b.src.charAt(a)));return null==c||null!=b.cbits&&b.cbits.get(a)?-1:c.matchInternal(a+1,b)},"~N,com.stevesoft.pat.Pthings");c$=B(com.stevesoft.pat, +"RegOpt");c$.opt=d(c$,"opt",function(a,b,c){if(null==a)return a;if(v(a,com.stevesoft.pat.Bracket)){var f=a;a=com.stevesoft.pat.FastBracket.process(f,b);a.next=f.next;a.parent=f.parent}else if(v(a,com.stevesoft.pat.oneChar)&&!b&&!c){var d=a;a=new com.stevesoft.pat.FastChar(d.c);a.next=d.next;a.parent=d.parent}else if(v(a,com.stevesoft.pat.Or)&&a.leftForm().equals("(?:")&&1==a.v.size())d=a,a=d.v.elementAt(0),a.setParent(null),a=com.stevesoft.pat.RegOpt.opt(a,b,c),a.add(d.next);else if(v(a,com.stevesoft.pat.Or)){d= +a;d.pv=null;var k=d.v;d.v=new java.util.Vector;f=new com.stevesoft.pat.Branch;f.parent=d.parent;for(var g=0;g=com.stevesoft.pat.FastBracket.getl(c.elementAt(d)).charCodeAt(0)){var n=c.elementAt(d),x=com.stevesoft.pat.FastBracket.min(com.stevesoft.pat.FastBracket.getl(k),com.stevesoft.pat.FastBracket.getl(n)),u=com.stevesoft.pat.FastBracket.max(com.stevesoft.pat.FastBracket.geth(k),com.stevesoft.pat.FastBracket.geth(n));f.setElementAt(k=com.stevesoft.pat.FastBracket.mkelem(x, +u),f.size()-1)}else k=c.elementAt(d),f.addElement(k);a.v=c=f}catch(D){if(y(D,com.stevesoft.pat.RegSyntax))D.printStackTrace();else throw D;}f=com.stevesoft.pat.FastBracket.neg(c);if(1==c.size())return a;if(1==f.size())return a.v=f,a.neg=!a.neg,a;c=com.stevesoft.pat.FastBracket.newbrack(c,a.neg);null==c&&(c=com.stevesoft.pat.FastBracket.newbrack(f,!a.neg));return null!=c?(c.parent=a.parent,c.next=a.next,c):a},"com.stevesoft.pat.Bracket,~B");c$.newbrack=d(c$,"newbrack",function(a,b){var c=new com.stevesoft.pat.FastBracket(b); +c.v=a;if(0==a.size())return null;c.$min=com.stevesoft.pat.FastBracket.getl(a.elementAt(0)).charCodeAt(0);c.$max=com.stevesoft.pat.FastBracket.geth(a.elementAt(a.size()-1)).charCodeAt(0);if(256>=c.$max-c.$min){c.bs=new java.util.BitSet(c.$max-c.$min+1);for(var f=0;fb?a:b},"~S,~S");c$.getl=d(c$,"getl",function(a){return v(a,com.stevesoft.pat.Range)?a.lo:a.c},"~O");c$.geth=d(c$,"geth",function(a){return v(a,com.stevesoft.pat.Range)?a.hi:a.c},"~O");e(c$,"matchInternal",function(a,b){if(a>=b.src.length()||this.Masked(a,b))return-1;var c=b.src.charAt(a);return(new Boolean(this.neg^(c.charCodeAt(0)>=this.$min&&c.charCodeAt(0)<=this.$max&&this.bs.get(c.charCodeAt(0)-this.$min)))).valueOf()? +this.nextMatch(a+1,b):-1},"~N,com.stevesoft.pat.Pthings")});q(null,"java.util.BitSet",["java.lang.IndexOutOfBoundsException","$.NegativeArraySizeException","$.StringBuffer","java.util.Arrays"],function(){c$=s(function(){this.bits=null;r(this,arguments)},java.util,"BitSet",null,[Cloneable,java.io.Serializable]);m(c$,function(){this.construct(32)});m(c$,function(a){if(0>a)throw new NegativeArraySizeException;var b=a>>>5;0!=(a&4)&&++b;this.bits=E(b,0)},"~N");d(c$,"and",function(a){var b=Math.min(this.bits.length, +a.bits.length),c;for(c=0;c>1&1431655765)+(c&1431655765),c=(c>>2&858993459)+(c&858993459),c=(c>>4&252645135)+(c&252645135),c=(c>>8&16711935)+(c&16711935),a+=(c>> +16&65535)+(c&65535)))}return a});d(c$,"clear",function(){java.util.Arrays.fill(this.bits,0)});d(c$,"clear",function(a){var b=a>>5;this.ensure(b);this.bits[b]&=~(1<a||a>b)throw new IndexOutOfBoundsException;if(a!=b){var c=a>>>5,f=b>>>5;this.ensure(f);if(c==f)this.bits[f]&=(1<>5;this.ensure(b);this.bits[b]^=1<a||a>b)throw new IndexOutOfBoundsException; +if(a!=b){var c=a>>>5,f=b>>>5;this.ensure(f);if(c==f)this.bits[f]^=-1<>5;return b>=this.bits.length?!1:0!=(this.bits[b]&1<a||a>b)throw new IndexOutOfBoundsException;var c=new java.util.BitSet(b-a),f=a>>>5;if(f>=this.bits.length)return c;var d=a&4,k=b>>>5;if(0==d){var g=Math.min(k-f+1,this.bits.length-f);System.arraycopy(this.bits, +f,c.bits,0,g);k>>d|this.bits[f+1]<d&&(c.bits[j++]=this.bits[f]>>>d);ka)return 0;var b=this.bits[a];for(a=32*(a+1);0==(b&2147483648);)--a,b<<=1;return a});d(c$,"nextClearBit",function(a){for(var b=a>>5,c=1<>5,c=1<>5;this.ensure(b);this.bits[b]|=1<a||a>b)throw new IndexOutOfBoundsException;if(a!=b){var c=a>>>5,f=b>>>5;this.ensure(f); +if(c==f)this.bits[f]|=-1<k;++k)0!=(d&f)&&(b||a.append(", "),a.append(32*c+k),b=!1),f<<=1}return a.append("}").toString()});d(c$,"xor", +function(a){this.ensure(a.bits.length-1);for(var 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a.append(this.string.subSequence(this.appendPos,this.string.length()))}, +"StringBuffer");d(c$,"replaceFirst",function(a){this.reset();if(this.find()){var b=new StringBuffer;this.appendReplacement(b,a);return this.appendTail(b).toString()}return this.string.toString()},"~S");d(c$,"replaceAll",function(a){var b=new StringBuffer;for(this.reset();this.find();)this.appendReplacement(b,a);return this.appendTail(b).toString()},"~S");d(c$,"pattern",function(){return this.pat});d(c$,"group",function(a){return null==this.results||0>a||a>this.results.length?null:this.results[a]}, +"~N");d(c$,"group",function(){return this.group(0)});d(c$,"find",function(a){var b=this.string.length();if(0>a||a>b)throw new IndexOutOfBoundsException("Out of bound "+a);this.findAt(a);return!1},"~N");d(c$,"findAt",($fz=function(){return-1},$fz.isPrivate=!0,$fz),"~N");d(c$,"find",function(){this.results=this.pat.regexp.exec(this.string.subSequence(this.leftBound,this.rightBound));return null!=this.results});d(c$,"start",function(){var a=0,a=this.pat.regexp.lastIndex;return a-=this.results[0].length}, +"~N");d(c$,"end",function(){return this.pat.regexp.lastIndex},"~N");d(c$,"matches",function(){return this.find()});c$.quoteReplacement=d(c$,"quoteReplacement",function(a){if(0>a.indexOf("\\")&&0>a.indexOf("$"))return a;for(var b=new StringBuffer(2*a.length),c,f=a.length,d=0;d=b)c=5;else if("%"==a.charAt(f))if(f=b?c=5:" "==a.charAt(f)?this.show_space= 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jalview.analysis.Conservation(this.groupName,jalview.schemes.ResidueProperties.propHash,3,this.sequences,this.startRes,this.endRes+1);b.calculate();b.verdict(!1,this.consPercGaps); +null!=this.conservation&&this._updateConservationRow(b);null!=this.cs&&this.cs.conservationApplied()&&this.cs.setConservation(b)}null!=this.cs&&this.cs.alignmentChanged(null!=this.context?this.context:this,null)}catch(c){if(y(c,OutOfMemoryError))System.out.println("Out of memory loading groups: "+c);else throw c;}});d(c$,"_updateConservationRow",function(a){null==this.conservation&&this.getConservation();this.conservation.label="Conservation for "+this.getName();this.conservation.description="Conservation for group "+ +this.getName()+" less than "+this.consPercGaps+"% gaps";var b=null!=this.conservation.annotations?this.endResthis.width)this.width= +b.getLength(),a=!1;return this.width});d(c$,"setOutlineColour",function(a){this.outlineColour=a},"java.awt.Color");d(c$,"getOutlineColour",function(){return 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Integer(g));c.put("R",u);p=100*g/x;c.put("G",new Float(p));0=c.length||null==(n=c[f]))a.annotations[f]=null;else{var x=n.get(e?"N":"G");if(null==x)a.annotations[f]= +null;else{var x=x.floatValue(),u=n.get("R").toString(),m=new StringBuilder(64);1=c?null:new jalview.util.Format("%3."+(c-1)+"f")},"~N");c$.extractProfile=d(c$,"extractProfile",function(a,c){var f=w(64,0),d=a.get("P");if(null==d)return null;for(var e=N(d[0].length,"\x00"),g=Q(d[0].length,0),h=0;h= +a;a=String.fromCharCode(a.charCodeAt(0)+1))jalview.analysis.AAFrequency.CHARS[a.charCodeAt(0)-65]=String.valueOf(a)});p("jalview.analysis");c$=B(jalview.analysis,"CodingUtils");c$.encodeCodon=d(c$,"encodeCodon",function(a){return null==a?-1:jalview.analysis.CodingUtils.encodeCodon(a[2])+(jalview.analysis.CodingUtils.encodeCodon(a[1])<<2)+(jalview.analysis.CodingUtils.encodeCodon(a[0])<<4)},"~A");c$.encodeCodon=d(c$,"encodeCodon",function(a){var b=-2147483648;switch(a){case "A":case "a":b=0;break; +case "C":case "c":b=1;break;case 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java.util.Hashtable;for(var n="-";"Z">n;n=String.fromCharCode(n.charCodeAt(0)+1))if(d[n.charCodeAt(0)]>c){g=String.valueOf(n); +for(h=this.propHash.keys();h.hasMoreElements();)e=h.nextElement(),b=this.propHash.get(e),a.containsKey(e)?!1==a.get(e).equals(b.get(g))&&a.put(e,new Integer(-1)):b.containsKey(g)?a.put(e,b.get(g)):a.put(e,b.get("-"))}0=this.sequences[g].getLength()?b++:(j=this.sequences[g].getCharAt(a),jalview.util.Comparison.isGap(j)?b++:(f++,1==f?(e=j, +c++):e==j&&c++));d[0]=f==c?1:0;d[1]=b;return d},"~N");d(c$,"verdict",function(a,b){for(var c=new StringBuffer,f,d,e,g,h,j,n=0;nf){h=this.total[n-this.start];g=0;for(j=h.keys();j.hasMoreElements();)f=j.nextElement(),d=h.get(f),a?1==d.intValue()&&(this.consSymbs[n-this.start]= +f+" "+this.consSymbs[n-this.start],g++):-1!=d.intValue()&&(this.consSymbs[n-this.start]=0==d.intValue()?this.consSymbs[n-this.start]+" !"+f:f+" "+this.consSymbs[n-this.start],g++);10>g?c.append(""+g):c.append(1==e[0]?"*":"+")}else 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+d(c$,"showAll",function(a){for(var b=new java.util.ArrayList,c=0;c=this.hiddenSequences.length&& +(d=this.hiddenSequences.length-1);d>f;d--){var e=this.hiddenSequences[d];this.hiddenSequences[d]=null;null!=e&&(0a.size()?11:2*a.size())]);var b;for(a=a.iterator();a.hasNext()&&((b=a.next())||1);)this.add(b)},"java.util.Collection");e(c$, +"createBackingMap",function(a,b){return new java.util.LinkedHashMap(a,b)},"~N,~N")});q(["java.util.HashMap"],"java.util.LinkedHashMap",["java.lang.IllegalStateException","java.util.AbstractCollection","$.AbstractSet","java.util.MapEntry.Type","java.util.NoSuchElementException"],function(){c$=s(function(){this.accessOrder=!1;this.tail=this.head=null;r(this,arguments)},java.util,"LinkedHashMap",java.util.HashMap);m(c$,function(){t(this,java.util.LinkedHashMap);this.accessOrder=!1;this.head=null});m(c$, 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Float(c)).floatValue()}catch(f){if(!y(f,Exception))throw f; +}1>=this.widthScale&&(System.err.println("Invalid alignment character width scaling factor ("+this.widthScale+"). Ignoring."),this.widthScale=1);jalview.bin.JalviewLite.debug&&System.err.println("Alignment character width scaling factor is now "+this.widthScale)}c=b.heightScale;if(null!=c){try{this.heightScale=(new Float(c)).floatValue()}catch(d){if(!y(d,Exception))throw d;}1>=this.heightScale&&(System.err.println("Invalid alignment character height scaling factor ("+this.heightScale+"). Ignoring."), +this.heightScale=1);jalview.bin.JalviewLite.debug&&System.err.println("Alignment character height scaling factor is now "+this.heightScale)}}this.setFont(this.font);this.MAC=jalview.util.Platform.isAMac();null!=b&&(this.setShowJVSuffix(b.getDefaultParameter("showFullId",this.getShowJVSuffix())),this.setShowAnnotation(b.getDefaultParameter("showAnnotation",this.isShowAnnotation())),this.showConservation=b.getDefaultParameter("showConservation",this.showConservation),this.showQuality=b.getDefaultParameter("showQuality", +this.showQuality),this.showConsensus=b.getDefaultParameter("showConsensus",this.showConsensus),this.setShowUnconserved(b.getDefaultParameter("showUnconserved",this.getShowUnconserved())),this.setScaleProteinAsCdna(b.getDefaultParameter("scaleProteinAsCdna",this.isScaleProteinAsCdna())),c=b.upperCase,null!=c&&c.equalsIgnoreCase("bold")&&this.setUpperCasebold(!0),this.sortByTree=b.getDefaultParameter("sortByTree",this.sortByTree),this.setFollowHighlight(b.getDefaultParameter("automaticScrolling",this.isFollowHighlight())), +this.followSelection=this.isFollowHighlight(),this.showSequenceLogo=b.getDefaultParameter("showSequenceLogo",this.showSequenceLogo),this.normaliseSequenceLogo=b.getDefaultParameter("normaliseSequenceLogo",b.getDefaultParameter("normaliseLogo",this.normaliseSequenceLogo)),this.showGroupConsensus=b.getDefaultParameter("showGroupConsensus",this.showGroupConsensus),this.showGroupConservation=b.getDefaultParameter("showGroupConservation",this.showGroupConservation),this.showConsensusHistogram=b.getDefaultParameter("showConsensusHistogram", +this.showConsensusHistogram));null!=b&&(c=b.defaultColour,null==c&&(c=b.userDefinedColour,null!=c&&(c="User Defined")),null!=c&&(this.globalColourScheme=jalview.schemes.ColourSchemeProperty.getColour(this.alignment,c),null!=this.globalColourScheme&&this.globalColourScheme.setConsensus(this.hconsensus)),null!=b.userDefinedColour&&this.globalColourScheme.parseAppletParameter(b.userDefinedColour));this.initAutoAnnotation()},"jalview.datamodel.AlignmentI,jalview.bin.JalviewLite");d(c$,"getConsensusSeq", +function(){null==this.consensus&&this.updateConsensus(null);if(null==this.consensus)return null;for(var a=new StringBuilder(this.consensus.annotations.length),b=0;bthis.colSel.size()||(this.colSel.hideSelectedColumns(),this.setSelectionGroup(null))});d(c$,"hideColumns",function(a,b){a==b?this.colSel.hideColumns(a):this.colSel.hideColumns(a,b)},"~N,~N"); +d(c$,"showColumn",function(a){this.colSel.revealHiddenColumns(a)},"~N");d(c$,"showAllHiddenColumns",function(){this.colSel.revealAllHiddenColumns()});d(c$,"showAllHiddenSeqs",function(){if(0this.selectionGroup.getSize())){var a=this.selectionGroup.getSequencesInOrder(this.alignment);this.hideSequence(a);this.setSelectionGroup(null)}});d(c$,"hideSequence",function(a){if(null!=a){for(var b=0;bc)){null==this.hiddenRepSequences&&(this.hiddenRepSequences=new java.util.Hashtable);this.hiddenRepSequences.put(a, +b);for(var f=Array(c-1),d=0,e=0;eb&&(d=b)),c.add(w(-1,[f,d])),null!=this.colSel&&this.colSel.hasHiddenColumns()&& +(f=this.colSel.adjustForHiddenColumns(d),f=this.colSel.getHiddenBoundaryLeft(f)+1);while(da&&c.setEndRes(a-1);null!=this.selectionGroup&&this.selectionGroup.getEndRes()>a&&this.selectionGroup.setEndRes(a-1);this.resetAllColourSchemes();this.calculator.restartWorkers()},"jalview.api.AlignmentViewPanel");d(c$,"resetAllColourSchemes",function(){var a=this.globalColourScheme;null!=a&&(a.alignmentChanged(this.alignment,this.hiddenRepSequences),a.setConsensus(this.hconsensus),a.conservationApplied()&&a.setConservation(jalview.analysis.Conservation.calculateConservation("All", +jalview.schemes.ResidueProperties.propHash,3,this.alignment.getSequences(),0,this.alignment.getWidth(),!1,this.getConsPercGaps(),!1)));for(var b,a=this.alignment.getGroups().iterator();a.hasNext()&&((b=a.next())||1);)null!=b.cs&&b.cs.alignmentChanged(b,this.hiddenRepSequences),b.recalcConservation()});d(c$,"initAutoAnnotation",function(){null==this.hconsensus&&!this.$isDataset&&(this.alignment.isNucleotide()?this.initRNAStructure():(this.initConservation(),this.initQuality()),this.consensus=new jalview.datamodel.AlignmentAnnotation("Consensus", +"PID",Array(1),0,100,1),this.initConsensus(this.consensus),this.initComplementConsensus())});d(c$,"initComplementConsensus",function(){if(!this.alignment.isNucleotide()){var a=this.alignment.getCodonFrames();null!=a&&!a.isEmpty()&&(this.complementConsensus=new jalview.datamodel.AlignmentAnnotation("cDNA Consensus","PID for cDNA",Array(1),0,100,1),this.initConsensus(this.complementConsensus))}});d(c$,"initConsensus",function(a){a.hasText=!0;a.autoCalculated=!0;this.showConsensus&&this.alignment.addAnnotation(a)}, +"jalview.datamodel.AlignmentAnnotation");d(c$,"initConservation",function(){this.showConservation&&null==this.conservation&&(this.conservation=new jalview.datamodel.AlignmentAnnotation("Conservation","Conservation of total alignment less than "+this.getConsPercGaps()+"% gaps",Array(1),0,11,1),this.conservation.hasText=!0,this.conservation.autoCalculated=!0,this.alignment.addAnnotation(this.conservation))});d(c$,"initQuality",function(){this.showQuality&&null==this.quality&&(this.quality=new jalview.datamodel.AlignmentAnnotation("Quality", +"Alignment Quality based on Blosum62 scores",Array(1),0,11,1),this.quality.hasText=!0,this.quality.autoCalculated=!0,this.alignment.addAnnotation(this.quality))});d(c$,"initRNAStructure",function(){this.alignment.hasRNAStructure()&&null==this.strucConsensus&&(this.strucConsensus=new jalview.datamodel.AlignmentAnnotation("StrucConsensus","PID",Array(1),0,100,1),this.strucConsensus.hasText=!0,this.strucConsensus.autoCalculated=!0,this.showConsensus&&this.alignment.addAnnotation(this.strucConsensus))}); +e(c$,"calcPanelHeight",function(){var a=this.getAlignment().getAlignmentAnnotation(),b=0,c=this.getCharHeight();if(null!=a)for(var f=new java.util.BitSet,d,e=0;ethis.alignment.getWidth()-1&&(a=this.alignment.getWidth()-1);0>a&&(a=0);this.endRes=a},"~N");d(c$,"setEndSeq",function(a){a>this.alignment.getHeight()&&(a=this.alignment.getHeight());0>a&&(a=0);this.endSeq=a},"~N");d(c$,"getEndSeq",function(){return this.endSeq}); +d(c$,"findComplementScrollTarget",function(a){var b=this.getCodingComplement();if(null==b||!b.isFollowHighlight())return 0;b=!this.getAlignment().isNucleotide()?this.getAlignment():b.getAlignment();if(null==b)return 0;for(var b=b.getCodonFrames(),c=0,f=null,d=this.getStartRes()+F((this.getEndRes()-this.getStartRes())/2),e=this.getAlignment().getHiddenSequences(),g=this.getStartSeq();g=b&&(b=a,b|=b>>>1,b|=b>>>2,b|=b>>>4,b|=b>>>8,b|=b>>>16,b++,0>b&&(b>>>=1));this.elements= +Array(b)},"~N");d(c$,"doubleCapacity",function(){var a=this.head,b=this.elements.length,c=b-a,f=b<<1;if(0>f)throw new IllegalStateException("Sorry, deque too big");f=Array(f);System.arraycopy(this.elements,a,f,0,c);System.arraycopy(this.elements,0,f,c,a);this.elements=f;this.head=0;this.tail=b});d(c$,"copyElements",function(a){if(this.headthis.tail){var b=this.elements.length-this.head;System.arraycopy(this.elements, +this.head,a,0,b);System.arraycopy(this.elements,0,a,b,this.tail)}return a},"~A");m(c$,function(){t(this,java.util.ArrayDeque,[]);this.elements=Array(16)});m(c$,function(a){t(this,java.util.ArrayDeque,[]);this.allocateElements(a)},"~N");m(c$,function(a){t(this,java.util.ArrayDeque,[]);this.allocateElements(a.size());this.addAll(a)},"java.util.Collection");e(c$,"addFirst",function(a){if(null==a)throw new NullPointerException;this.elements[this.head=this.head-1&this.elements.length-1]=a;this.head==this.tail&& +this.doubleCapacity()},"~O");e(c$,"addLast",function(a){if(null==a)throw new NullPointerException;this.elements[this.tail]=a;(this.tail=this.tail+1&this.elements.length-1)==this.head&&this.doubleCapacity()},"~O");e(c$,"offerFirst",function(a){this.addFirst(a);return!0},"~O");e(c$,"offerLast",function(a){this.addLast(a);return!0},"~O");e(c$,"removeFirst",function(){var a=this.pollFirst();if(null==a)throw new java.util.NoSuchElementException;return a});e(c$,"removeLast",function(){var a=this.pollLast(); +if(null==a)throw new java.util.NoSuchElementException;return a});e(c$,"pollFirst",function(){var a=this.head,b=this.elements[a];if(null==b)return null;this.elements[a]=null;this.head=a+1&this.elements.length-1;return b});e(c$,"pollLast",function(){var a=this.tail-1&this.elements.length-1,b=this.elements[a];if(null==b)return null;this.elements[a]=null;this.tail=a;return b});e(c$,"getFirst",function(){var a=this.elements[this.head];if(null==a)throw new java.util.NoSuchElementException;return a});e(c$, +"getLast",function(){var a=this.elements[this.tail-1&this.elements.length-1];if(null==a)throw new java.util.NoSuchElementException;return a});e(c$,"peekFirst",function(){return this.elements[this.head]});e(c$,"peekLast",function(){return this.elements[this.tail-1&this.elements.length-1]});e(c$,"removeFirstOccurrence",function(a){if(null==a)return!1;for(var b=this.elements.length-1,c=this.head,f;null!=(f=this.elements[c]);){if(a.equals(f))return this.$delete(c),!0;c=c+1&b}return!1},"~O");e(c$,"removeLastOccurrence", +function(a){if(null==a)return!1;for(var b=this.elements.length-1,c=this.tail-1&b,f;null!=(f=this.elements[c]);){if(a.equals(f))return this.$delete(c),!0;c=c-1&b}return!1},"~O");e(c$,"add",function(a){this.addLast(a);return!0},"~O");e(c$,"offer",function(a){return this.offerLast(a)},"~O");d(c$,"remove",function(){return this.removeFirst()});e(c$,"poll",function(){return this.pollFirst()});e(c$,"element",function(){return this.getFirst()});e(c$,"peek",function(){return this.peekFirst()});e(c$,"push", +function(a){this.addFirst(a)},"~O");e(c$,"pop",function(){return this.removeFirst()});d(c$,"checkInvariants",function(){});d(c$,"$delete",function(a){this.checkInvariants();var b=this.elements,c=b.length-1,f=this.head,d=this.tail,e=a-f&c,g=d-a&c;if(e>=(d-f&c))throw new java.util.ConcurrentModificationException;if(eb&&(a[b]=null);return a},"~A");d(c$,"clone",function(){try{var a=K(this,java.util.ArrayDeque,"clone",[]);a.elements=java.util.Arrays.copyOf(this.elements,this.elements.length);return a}catch(b){if(y(b,CloneNotSupportedException))throw new AssertionError;throw b;}});c$.$ArrayDeque$DeqIterator$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.fence=this.cursor=0;this.lastRet=-1;r(this,arguments)},java.util.ArrayDeque,"DeqIterator",null,java.util.Iterator); +J(c$,function(){this.cursor=this.b$["java.util.ArrayDeque"].head;this.fence=this.b$["java.util.ArrayDeque"].tail});e(c$,"hasNext",function(){return this.cursor!=this.fence});e(c$,"next",function(){if(this.cursor==this.fence)throw new java.util.NoSuchElementException;var a=this.b$["java.util.ArrayDeque"].elements[this.cursor];if(this.b$["java.util.ArrayDeque"].tail!=this.fence||null==a)throw new java.util.ConcurrentModificationException;this.lastRet=this.cursor;this.cursor=this.cursor+1&this.b$["java.util.ArrayDeque"].elements.length- +1;return a});e(c$,"remove",function(){if(0>this.lastRet)throw new IllegalStateException;this.b$["java.util.ArrayDeque"].$delete(this.lastRet)&&(this.cursor=this.cursor-1&this.b$["java.util.ArrayDeque"].elements.length-1,this.fence=this.b$["java.util.ArrayDeque"].tail);this.lastRet=-1});c$=z()};c$.$ArrayDeque$DescendingIterator$=function(){A(self.c$);c$=s(function(){O(this,arguments);this.fence=this.cursor=0;this.lastRet=-1;r(this,arguments)},java.util.ArrayDeque,"DescendingIterator",null,java.util.Iterator); +J(c$,function(){this.cursor=this.b$["java.util.ArrayDeque"].tail;this.fence=this.b$["java.util.ArrayDeque"].head});e(c$,"hasNext",function(){return this.cursor!=this.fence});e(c$,"next",function(){if(this.cursor==this.fence)throw new java.util.NoSuchElementException;this.cursor=this.cursor-1&this.b$["java.util.ArrayDeque"].elements.length-1;var a=this.b$["java.util.ArrayDeque"].elements[this.cursor];if(this.b$["java.util.ArrayDeque"].head!=this.fence||null==a)throw new java.util.ConcurrentModificationException; +this.lastRet=this.cursor;return a});e(c$,"remove",function(){if(0>this.lastRet)throw new IllegalStateException;this.b$["java.util.ArrayDeque"].$delete(this.lastRet)||(this.cursor=this.cursor+1&this.b$["java.util.ArrayDeque"].elements.length-1,this.fence=this.b$["java.util.ArrayDeque"].head);this.lastRet=-1});c$=z()};G(c$,"MIN_INITIAL_CAPACITY",8)});p("java.util");q(["java.util.Queue"],"java.util.Deque",null,function(){M(java.util,"Deque",java.util.Queue)});p("jalview.datamodel");q(null,"jalview.datamodel.AlignmentView", +"jalview.datamodel.Alignment $.CigarArray $.ColumnSelection $.SeqCigar $.SequenceGroup jalview.util.MessageManager $.ShiftList java.lang.Error java.util.ArrayList $.Vector".split(" "),function(){c$=s(function(){this.contigs=this.sequences=null;this.firstCol=this.width=0;this.scGroups=null;this.$isNa=!1;H("jalview.datamodel.AlignmentView.ScGroup")||jalview.datamodel.AlignmentView.$AlignmentView$ScGroup$();this.selected=null;r(this,arguments)},jalview.datamodel,"AlignmentView");d(c$,"isNa",function(){return this.$isNa}); +m(c$,function(a,b,c,f,d){this.construct(new jalview.datamodel.CigarArray(a,f?b:null,d?c:null),d&&null!=c?c.getStartRes():0);this.$isNa=a.isNucleotide();null!=c&&0g||j.getEndRes()g&&j.setEndRes(g),j.setStartRes(j.getStartRes()-a+1),j.setEndRes(j.getEndRes()-a+1),h.add(j));e=h}a=Array(e.size());g=X(e.size(),!1);for(h=0;hc||n.getEndRes()c-b&&h[j].setEndRes(c-b)))}if(f&&null!=this.contigs){j=0;f=new jalview.util.ShiftList;d&&f.addShift(b, +-b);for(n=0;nc&&(x=c));n=f.shift(n);x=f.shift(x);h[j].setStartRes(n);h[j].setEndRes(x)}}for(b=0;b=this.width)return null;if(null!=this.contigs&&0=this.width)throw Error(jalview.util.MessageManager.getString("error.empty_view_cannot_be_updated"));if(null== +a)throw Error("nvismsa==null. use getAlignmentAndColumnSelection() instead.");if(null!=this.contigs&&0=u.getStart()&&f[m].setEnd(u.getEnd()));j++}g+=x}e=this.contigs[n+1]+this.contigs[n+2];for(m=0;m=x.getStart()&&f[m].setEnd(x.getEnd()));d.hideColumns(g,g+this.contigs[n+2]-1);g+=this.contigs[n+2]}if(j=e[m].getStart()&&f[m].setEnd(e[m].getEnd()),null!=u&&u.updateSequence(e[m],f[m]))}else if(e= +u.getStart()&&f[m].setEnd(u.getEnd()))}return E(-1,[f,d])}if(1!=a.length)throw Error(jalview.util.MessageManager.formatMessage("error.mismatch_between_visible_blocks_to_update_and_number_of_contigs_in_view",E(-1,[Integer.$valueOf(a.length).toString()])));return null!=a[0]?E(-1,[a[0],new jalview.datamodel.ColumnSelection]):this.getAlignmentAndColumnSelection(c)},"~A,~A,~S");d(c$,"getVisibleContigs",function(){if(null!=this.contigs&&0